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SULI Project Report: Mu2e otsdaq Documentation and Analytics

This report outlines the history of the CLFV puzzle, gives an overview of the Mu2e Experiment, and details the results of the DOE (Department of Energy)-funded SULI (Science Undergraduate Laboratory Internship) research completed over the summer 2024 on site at Fermilab. The project focused on the otsdaq software responsible for data acquisition. The project included drafting updated documentation for new users, including new procedures relevant for the Alma- Linux 9 operating system update, and the UPS package managing system replacement with Spack (scientific software package manager). A new art module (ReadTriggerCounts) to track trigger rates was created, with compatibility to be displayed via a Grafana server. The author also assisted in calorimeter cable installation in the detector hall.

Saarinen, Talia↗

The small protein SbtC is a functional component of the CO 2 concentrating mechanism in Synechocystis sp. PCC 6803

Oxygenic phototrophs fix CO 2 via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which shows relatively low CO 2 affinity and specificity. To circumvent low and fluctuating CO 2 concentrations in aquatic systems, cyanobacteria and algae have evolved sophisticated inorganic carbon (Ci) concentrating mechanisms (CCMs). Bicarbonate transporters such as SbtA play a crucial role in the cyanobacterial CCM and hence display multiple layers of tight regulation. Control of sbtA gene expression and corresponding transporter activity involves the PII-like protein SbtB, whose gene is frequently co-transcribed with sbtA. A previously non-annotated gene located upstream of the sbtAB operon in the model Synechocystis sp. PCC 6803 encodes the small protein SbtC, composed of 80 amino acids. Presence of SbtC was confirmed by immunoblotting of the sbtC-coding sequence fused to a Flag-tag. Similar to sbtAB , transcription of the sbtC locus is induced by low CO 2 availability; however, it is controlled independently. Mutation of the sbtC locus in a wild-type background produced only a mild phenotype, even under low CO 2 , but impaired diurnal growth resembled that of the mutant ΔsbtB . Biochemical analysis indicated a trimeric SbtABC complex in the membrane. Bicarbonate leakage from cells was strongly elevated when either sbtB or sbtC was deleted from recombinant Synechocystis strains harboring only SbtA as single Ci uptake system. Here, our results provide evidence that SbtC contributes to the formation of the SbtAB complex, thereby regulating bicarbonate exchange at the cytoplasmic membrane. Well-conserved SbtC-like proteins encoded in the neighborhood of sbtAB exist in many cyanobacterial genomes, pointing toward an important role in the cyanobacterial CCM.

Walke, Peter [Univ. of Rostock (Germany)] (ORCID:0↗

Design, synthesis, evaluation and X-ray structural studies of potent HIV-1 protease inhibitors containing substituted oxaspirocyclic carbamates as the P2 ligands

Here, we report here the design, synthesis and evaluation of a series of HIV-1 protease inhibitors that incorporate substituted oxaspirocyclic carbamate derivatives to serve as the P2 ligands. Various substituted ligand derivatives were synthesized in a racemic manner, using a tandem Prins/pinacol reaction as the key reaction. This reaction sets the relative stereochemistry of the oxaspirocyclic template in a highly diastereoselective manner. Reaction of the resulting ketone with enantiopure (S)-tert-butyl sulfinamide provided a convenient pathway to resolve the oxaspirocyclic ketone derivatives. The absolute stereochemical identity was determined by X-ray crystallography. The structure-activity studies demonstrate the effect of the stereochemistry of the oxaspirocyclic ring systems as well as the substitution effect on the aromatic ring. Several inhibitors exhibited potent HIV-1 protease inhibitory activity. One of these inhibitors displayed subnanomolar HIV-1 protease affinity and also exhibited potent antiviral activity. A high-resolution X-ray crystal structure of this inhibitor-bound HIV-1 protease show that the oxaspirocyclic P2 ligand forms an unconventional C–H⋯O bond with the backbone carboxyl group of Gly48’ and an interesting N–H … π interaction with the aromatic ring in the S2 subsite of HIV-1 protease active site.

Antiviral↗

Chlorocobaltate-Enabled Selective Separation of CoCl 2 from Mixed Chloride and Nitrate Salts of Mn, Co, and Ni

Described here is the effect of anionic metalates─chlorocobaltate and nitratocobaltate─on the heat-driven separation of the critical element cobalt from potentially competing transition metal salts. Resins bearing the hexadentate glycolamide receptor L (PS-L) exhibit sorption capacities, Q = 1.33 mmol/g for CoCl 2 and Q = 0.66 mmol/g for Co(NO 3 ) 2 , as inferred from sorption isotherm studies. This trend runs counter to the typical Hofmeister series for anion selectivity. Ion chromatographic analysis of a mixed CoCl 2 /Co(NO 3 ) 2 solution revealed an increase in chloride content from 55 mol % to 90 mol % after a single thermally driven catch-and-release cycle. This chloride-selective behavior was recapitulated in a mixed-metal cation, mixed-anion system containing the chloride and nitrate salts of Mn(II), Co(II), and Ni(II) at near-equimolar concentrations. PS-L also displayed enhanced selectivity for Co using this mixed stock solution as observed by ICP-OES. In contrast, for a nitrate-only solution containing Mn(II), Co(II), and Ni(II), PS-L showed increased affinity for Mn, with its proportion rising from 36.6 mol % to 58.1% after a single catch-and-release cycle. Density functional theory calculations support the suggestion that the enhanced uptake of Co(II) in chloride-rich media arises from the high thermodynamic stability of [CoCl 4 ] 2– , which facilitates its outer-sphere coordination to cationic resin-bound cobalt species. Single crystal X-ray crystallographic analyzes of L•MCl 2 (M = Mn, Co, Ni) and L•M(NO 3 ) 2 (M = Mn, Co) confirmed metal complexation by L in the solid state and the concomitant formation of metalate counteranions. Here, the present study highlights a relatively simple approach for separating cobalt from its transition metal congeners.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mu2e otsdaq Documentation and Online Reconstruction Analytics

This report outlines the results of the DOE-funded SULI (Science Undergraduate Laboratory Internship) research completed over the summer 2024 on site at Fermilab. The project focused on the \textit{otsdaq} software responsible for data acquisition. The project included drafting updated documentation for new users including new procedures relevant for the Alma-Linux 9 operating system update, and the UPS package managing system replacement with spack (scientific software package manager). A new \textit{art} module (ReadTriggerCounts) to track trigger rates was created, with compatibility to be displayed via a Grafana server. The author also assisted in calorimeter cable installation in the detector hall.

Saarinen, Talia↗

Organic superbases in Lewis pair catalyzed hydrogenations of imines

Organic superbases have recently emerged as powerful components in metal-free catalytic systems, yet their role in frustrated Lewis pair (FLP) catalyzed hydrogenation reactions remain underexplored. In this article, we investigate the diphosphazene superbases P 2 - t Bu (1) and P 2 -Et (2) as base components combined with electronically tunable boranes of formula 9-(X n -C 6 H 5-n )BBN, where X n = 4-NMe₂, 4-OMe, 4-Me, 4-H, 4-F, 4-OCF 3 , 4-CF 3 , 3,5-(CF3), in FLP-catalyzed hydrogenations of imines. While the more sterically encumbered base 1 forms persistent FLPs whose activity correlates with the hydride affinity of the borane, less hindered base 2 generates Lewis acid–base adducts and displays superior catalytic performance, especially with boranes of lower hydride affinity. A systematic screening identified the adduct 2/9-(4-MeO-C 6 H 4 )BBN as the most active catalytic system, achieving quantitative hydrogenation of N-benzylidene aniline at 80 °C and H 2 pressures as low as 40 bar in THF. Multinuclear NMR spectroscopic studies and DFT calculations support a mechanistic scenario in which reversible adduct formation and subsequent dissociation to the free acid–base pair precede heterolytic H₂ cleavage, with adduct stability and borane electrophilicity concurrently dictating catalytic activity. Under optimized conditions, the most active catalyst system, 2/9-(4-MeO-C 6 H 4 )BBN, hydrogenates a broad range of aldimines, including electron-rich 4-NMe₂ and push-pull substrates, mono- and bis-ortho-substituted imines, and selected heteroaryl imines, with excellent yields and selectivity. Collectively, these findings establish design principles for tuning BBN-derived FLP systems and expand the scope of metal-free hydrogenation catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rhizosphere Microbiome Diversity Potentially Supports Robust Nature of Field Pennycress ( Thlaspi arvense L.) in Dryland Cropping Systems of Eastern Washington

ABSTRACT Field pennycress ( Thlaspi arvense L.) is an annual in the Brassicaceae family and is currently being developed as an oilseed intermediate crop suitable for renewable biodiesel and jet fuel. It displays many desirable characteristics for this role including cold tolerance, a rapid life cycle, and a seed fatty acid profile conducive to bioenergy generation. These traits make field pennycress favorable for winter oilseed cultivation in the inland Pacific Northwest (iPNW). Simultaneously, intermediate crops are an increasingly recognized component of both agronomic sustainability and soil health management. Intermediate crops enhance soil microbial diversity, which benefits both soil and plant health. To understand the impact of field pennycress on soil microbial diversity, two natural accessions and seven experimental accessions were grown at three sites in Eastern Washington. Aboveground biomass and rhizosphere soil were then collected. Soil genomic DNA was extracted from rhizosphere samples and used to generate an amplicon library for bacterial (16S) and fungal (ITS) rRNA sequences. The resulting libraries were analyzed in QIIME2, which revealed that not only did the fad2 deficient line from the Spring32‐10 background have significantly increased aboveground biomass production compared to other pennycress genotypes, but also displayed significantly higher β‐diversity in the rhizosphere community specifically at the site experiencing the driest conditions. ANCOM analysis showed that multiple sequences similar to beneficial plant and soil health enhancing organisms such as Trichoderma spirale , Pseudomonas spp., and Methylobacterium goesingense were found to be enriched in the microbiome of the fad2 Spring32‐10 background also at that site. To add additional context to rhizosphere community data, root exudates from two pennycress genotypes were captured in magenta boxes and analyzed using HPLC. Future work will expand our understanding of the mechanisms by which field pennycress creates diversity in the rhizosphere, thus expanding our ability to cultivate this crop in the iPNW.

54 ENVIRONMENTAL SCIENCES↗

Electrically Reconfigurable Liquid Metal Nanophotonic Platform for Color Display and Imaging

Dynamically tunable optical materials and device architectures are essential for future photonic technologies, yet conventional solid metals lack the intrinsic tunability required for advanced functionalities. Gallium-based liquid metals (LMs) present an appealing alternative thanks to their distinctive mechanical and optical properties; however, their practical integration in tunable photonic elements remains largely unexplored. Here, in this study, an electrochemically controlled nanophotonic platform is demonstrated that integrates a dynamically reconfigurable LM ground plane with gold nanoantenna arrays within a microfluidic system, enabling precise and reversible modulation of optical resonances across the visible to mid-infrared spectral ranges. By employing moderate operational voltages (1.5–3.0 V), real-time tuning of high-resolution structural color patterns is achieved through nanoscale control of the interfacial gap between the LM and Au nanoantennas. This innovative platform facilitates electrically programmable, high-contrast color patterns suitable for dynamic optical displays, secure anti-counterfeiting labels, and imaging applications. Additionally, this platform enables tunable mid-infrared spectral responses, which may be utilized for chemical and biological sensing applications. This versatile integrated LM-based nanophotonic platform opens new paths toward multifunctional, actively tunable/reconfigurable photonic device and system technologies.

Imaging↗

Intrinsic Defect-Induced Local Semiconducting-to-Metallic Regions Within Monolayer 1T-TiS2 Displayed by First-Principles Calculations and Scanning Tunneling Microscopy

Using density functional theory (DFT) and scanning tunneling microscopy (STM), the intrinsic point defects, formation energy, and electronic structure of 1T-TiS2 were investigated. Defect systems include single-atom vacancies, interstitial and adatom additions, and direct atomic substitution. Using a collective approach for analyzing realistic systems for point defect investigation, we provide a more straightforward comparison to the experimental measurements, reproducing more realistic environmental conditions related to thin film growth. STM images are compared to computationally simulated electron density images to identify specific geometries that result from favorable point defects. DFT suggests that titanium interstitials are the most energetically favorable intrinsic defect, and sulfur vacancies are more likely to form than titanium vacancies within this realistic analysis, which is in agreement with STM data. A pristine, stoichiometric monolayer system is calculated to have a direct band gap of 0.422 eV, which varies based on local point defects. Local semiconducting-to-metallic electronic transitions are predicted to occur based on the presence of Ti interstitials.

Keeney, P. J.↗

Evidence for metal sources, fluid-mixing processes, and S isotope recycling within the feeder zone of an Irish type Zn-Pb deposit

The origin and evolution of fluids in Irish-type Zn-Pb deposits remains debated, particularly regarding the mobility of metals such as Cu and Ni, sources of sulphur, and the role of fluid mixing and replacement. The Lisheen Zn-Pb deposit, Ireland, offers a well-defined natural laboratory to investigate these questions. While most studies have focused on the Waulsortian Limestone Formation, the primary sulphide host, less is known about mineralisation in underlying units, such as the Lisduff Oolite Member (LOM). The LOM displays enrichment in Cu and Ni and displays intense replacement textures compared to other hosts at Lisheen, making it an ideal target for studying metal mobility and sulphur recycling in carbonate-hosted systems. Through characterising and studying LOM-hosted sulphides, valuable insights into mineralisation processes, especially related to Cu-Ni metals, can be defined. This study integrates petrography, EMPA, and in situ sulphur isotope (δ 34 S) analysis to investigate sulphide paragenesis, mineral chemistry, and fluid evolution across LOM ore zones. Results reveal a multistage mineralising system involving extensive replacement of early pyrite (Py0, δ 34 S = −28.4 to −21.9 ‰) by sphalerite and galena, with zoned pyrite (Py1) enriched in As-Cu-Ni-Tl. The δ 34 S values and trace element trends indicate mixing between hydrothermal and bacteriogenic sulphur-rich fluids, with evidence for sulphur recycling during replacement. Pyrite textures and compositions capture this evolving fluid regime, with trace element enrichment linked to paragenetic stage. The steel ore region, adjacent to major fault intersections, records intense hydrothermal fluid interaction, hosting Ni- and As-rich phases such as nickeline, gersdorffite, and arsenopyrite. These findings highlight the importance of structural controls and fluid mixing in metal transport and deposition, positioning the LOM as a key stratigraphic unit for understanding ore-forming processes in Irish-type systems. These results have implications for targeting similar carbonate-hosted systems globally, especially where deeper or structurally complex ore zones remain underexplored.

58 - GEOSCIENCES↗

Spin-Charge-Lattice Coupling across the Charge Density Wave Transition in a Kagome Lattice Antiferromagnet

Understanding spin and lattice excitations in a metallic magnetic ordered system forms the basis to unveil the magnetic and lattice exchange couplings and their interactions with itinerant electrons. Kagome lattice antiferromagnet FeGe is interesting because it displays a rare charge density wave (CDW) deep inside the antiferromagnetic ordered phase that interacts with the magnetic order. Here, we use neutron scattering to study the evolution of spin and lattice excitations across the CDW transition 𝑇 CDW in FeGe. While spin excitations below ∼100 meV can be well described by spin waves of a spin-1 Heisenberg Hamiltonian, spin excitations at higher energies are centered around the Brillouin zone boundary and extend up to ∼180 meV consistent with quasiparticle excitations across spin-polarized electron-hole Fermi surfaces. Furthermore, 𝑐-axis spin wave dispersion and Fe-Ge optical phonon modes show a clear hardening below 𝑇 CDW due to spin-charge-lattice coupling but with no evidence of a phonon Kohn anomaly. By comparing our experimental results with density functional theory calculations in absolute units, we conclude that FeGe is a Hund’s metal in the intermediate correlated regime where magnetism has contributions from both itinerant and localized electrons arising from spin polarized electronic bands near the Fermi level.

charge density waves↗

A Study on the Impact of Temperature-Dependent Ferroelectric Switching Behavior in 3D Memory Architecture

The flourishing development of neural networks that require exponentially growing amounts of data has presented an elevated demand for memory footprint. To address this, researchers have been exploring hardware accelerators with innovative memory architectures like 3D memory. These 3D memory architectures offer enhanced storage capacity and processing capabilities, at a cost of rising on-chip temperature during operation. Hafnium Zirconium Oxide (HZO) based Ferroelectric Random Access Memory (FeRAM) is a promising nonvolatile memory candidate in neural network hardware accelerators for its outstanding write performance and reliability. However, its implementation in the architecture regarding the temperature-dependent ferroelectric switching behavior has not been well studied. In this work, we study the thermal impacts on polarization switching through experimental devices and simulation results. We conduct the circuit and architecture-level simulations to showcase that one can exploit this temperature rise to reduce FeRAM's write voltage and write energy due to its unique temperature-activated polarization switching mechanisms. As the on-chip temperature increases to 351K (ambient temperature at 300K) due to neural network workloads, the access energy per bit can be reduced by 27.6% when a dynamic write voltage is applied.

36 MATERIALS SCIENCE↗

Interfacial Ice Density Fluctuations Inform Surface Ice-Philicity

The propensity of a surface to nucleate ice or bind to ice is governed by its ice-philicity─its relative preference for ice over liquid water. However, the relationship between the features of a surface and its ice-philicity is not well understood, and for surfaces with chemical or topographical heterogeneity, such as proteins, their ice-philicity is not even well-defined. In the analogous problem of surface hydrophobicity, it has been shown that hydrophobic surfaces display enhanced low water-density (vapor-like) fluctuations in their vicinity. To interrogate whether enhanced ice-like fluctuations are similarly observed near ice-philic surfaces, here we use molecular simulations and enhanced sampling techniques. Using a family of model surfaces for which the wetting coefficient, k , has previously been characterized, we show that the free energy of observing rare interfacial ice-density fluctuations decreases monotonically with increasing k . By utilizing this connection, we investigate a set of fcc systems and find that the (110) surface is more ice-philic than the (111) or (100) surfaces. By additionally analyzing the structure of interfacial ice, we find that all surfaces prefer to bind to the basal plane of ice, and the topographical complementarity of the (110) surface to the basal plane explains its higher ice-philicity. Using enhanced interfacial ice-like fluctuations as a measure of surface ice-philicity, we then characterize the ice-philicity of chemically heterogeneous and topologically complex systems. In particular, we study the spruce budworm antifreeze protein (sbwAFP), which binds to ice using a known ice-binding site (IBS) and resists engulfment using nonbinding sites of the protein (NBSs). We find that the IBS displays enhanced interfacial ice-density fluctuations and is therefore more ice-philic than the two NBSs studied. We also find the two NBSs are similarly ice-phobic. By establishing a connection between interfacial ice-like fluctuations and surface ice-philicity, our findings thus provide a way to characterize the ice-philicity of heterogeneous surfaces.

crystals↗

Beyond Component Optimization: Systems Level Biodesign for Lanthanide Recovery

Global demand for lanthanides (Ln) is projected to rise sharply over the next decade, while geographically concentrated supply chains and the low concentrations and matrix complexity of secondary feedstocks limit the reach of conventional hydro- and pyrometallurgical separation. Engineered biological systems offer a selective, low-energy alternative, and component-level advances in Ln-binding proteins, AI-designed selective scaffolds, and cell-surface display platforms now rival synthetic chelators in affinity and selectivity. These components, however, remain functionally isolated. Currently, there are no engineered chassis coupling recognition, intracellular trafficking, accumulation, and controlled release into an end-to-end pipeline. Here, we outline how new biodesign strategies and chassis selection must move beyond bioleaching to encompass the full recovery pathway. Achieving this requires integrating AI/ML-guided design, genome-scale build tools, high-throughput phenotyping, and biophysical transport modeling within a Design–Build–Test–Learn cycle tuned to recognition, trafficking, accumulation, and release.

Biodesign↗

Tetrel Bond-Mediated Photophysical Modulation and Fluoride Recognition in Carbazole-Organosilanes

Silicon-centered orbitals are typically regarded as electronically inert in donor–acceptor systems. Here, we show that silole-based carbazole–silane architectures can render these orbitals electronically relevant, enabling modulation of excited-state behavior and anion-responsive photophysics. Two carbazole–Dipp–silanes exhibit identical carbazole-localized LE singlet emission in solution yet diverge markedly in the solid state: one compound displays a broad long-wavelength emission band in the prompt spectrum and enhanced long-lived emission consistent with a triplet-derived excited state, likely arising from a combination of intramolecular structural locking and solid-state packing effects, whereas the more flexible analogue remains predominantly LE-emissive. Fluoride coordination further differentiates the two systems, producing ratiometric red-shifted emission in one case and fluorescence quenching in the other through a fully reversible coordination process. These results identify σ*(Si–Ar) orbitals as tunable contributors to excited-state landscapes in organosilane luminophores and suggest a broader design strategy for controlling excited-state behavior in tetrel-based photofunctional systems.

Haque, Md Hasanul↗

Effects of dimensionality on the electronic structure of Ruddlesden-Popper chromates Sr n+1 ⁢Cr n ⁢O 3⁢n+1

Transition-metal oxides host a wide variety of electronic phenomena that can be significantly influenced by the effective dimensionality of the system under consideration. These include charge, spin, and orbital orderings, as well as unconventional superconductivity. In this context, the Ruddlesden-Popper chromates Sr n+1 Cr n O 3n+1 emerge as a particularly intriguing series of materials. Formally, the chromium atom displays a rather special 4+ oxidation state throughout the entire series. However, the effective dimensionality changes from quasi-2D to 3D as n increases from 1 to ∞. As a result, the insulating antiferromagnetic behavior observed for n = 1, 2, 3 transforms into itinerant antiferromagnetism with reduced transition temperature for the n = ∞ end member of the series, i.e., the perovskite SrCrO 3 . Further, distinct orbital orderings with exotic singlet states have been predicted for these systems. However, the lack of single-crystal bulk or thin-film samples has made experimental progress difficult. Here we demonstrate the synthesis of thin films of the perovskite SrCrO 3 and the associated layered chromates via oxide molecular beam epitaxy for n = 1 to n = 5. Our electrical transport measurements reveal a gradual evolution from a strongly insulating state in Sr 2 CrO 4 to a metallic state in the end member SrCrO 3 . X-ray absorption spectroscopy measurements demonstrate a varying hybridization strength of the Cr 4+ valence electrons across the series, helping to explain the trend in conduction. Finally, density functional theory calculations further confirm the observed transport trend and identify additional distortions present in the system.

36 MATERIALS SCIENCE↗

Krylov complexity in mixed phase space

We investigate the Krylov complexity of thermofield double states in systems with mixed phase space, uncovering a direct correlation with the Brody distribution, which interpolates between Poisson and Wigner statistics. Our analysis spans two-dimensional random matrix models featuring (I) GOE-Poisson and (II) GUE-Poisson transitions and extends to higher-dimensional cases, including a stringy matrix model (GOE-Poisson) and the mass-deformed SYK model (GUE-Poisson). Krylov complexity consistently emerges as a reliable marker of quantum chaos, displaying a characteristic peak in the chaotic regime that gradually diminishes as the Brody parameter approaches zero, signaling a shift toward integrability. These results establish Krylov complexity as a powerful diagnostic of quantum chaos and highlight its interplay with eigenvalue statistics in mixed phase systems.

chaos & nonlinear dynamics↗

Dynamically Chiral Expanded Helicenes

Expanded helicenes are a class of chiral nanographenes with a screw-shaped skeleton and a larger diameter than their classical ortho-fused counterparts. The flexibility of this internal cavity results in helicenes that are often difficult to isolate as single enantiomers. Expanded helicenes are therefore an intriguing target for exploration of dynamic chirality, a phenomenon resulting from introduction of chiral auxiliaries to control structure in a racemic system. This contribution describes installation of chiral amine substituents into the cavity of a diformyl expanded [11]-helicene by mild, efficient, and reversible imine condensations. The resulting helicenes display strong molar circular dichroism up to |Δε| = 300 M -1 cm -1 and absorption dissymmetry factors of |g abs | = 0.010. The magnitude of circular dichroism can be varied by using different chiral amine substituents, which is correlated to the diastereomeric ratios of the helicenes. In conclusion, this is the first instance of dynamic chirality being used to observe a chiroptic response in expanded helicenes and is a significant synthetic improvement over methods which require conventional enantiomer resolution.

Rothenberger, August J. [University of California,↗