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32 records · Page 2

Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease

ABCA4 is an ATP-binding cassette (ABC) transporter that flips N-retinylidene-phosphatidylethanolamine (N-Ret-PE) from the lumen to the cytoplasmic leaflet of photoreceptor membranes. Loss-of-function mutations cause Stargardt disease (STGD1), a macular dystrophy associated with severe vision loss. To define the mechanisms underlying substrate binding and STGD1, we determine the cryo-EM structure of ABCA4 in its substrate-free and bound states. The two structures are similar and delineate an elongated protein with the two transmembrane domains (TMD) forming an outward facing conformation, extended and twisted exocytoplasmic domains (ECD), and closely opposed nucleotide binding domains. N-Ret-PE is wedged between the two TMDs and a loop from ECD1 within the lumen leaflet consistent with a lateral access mechanism and is stabilized through hydrophobic and ionic interactions with residues from the TMDs and ECDs. Our studies provide a framework for further elucidating the molecular mechanism associated with lipid transport and disease and developing promising disease interventions.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of ZnO and PEDOT:PSS charge selective layers on photovoltage of cuprous oxide (Cu 2 O) heterojunction solar cells

Electrochemical deposition (ECD) of Cu 2 O provides a scalable and low temperature pathway to solar cells with a theoretical high energy conversion efficiency of 23%, based on the 2.0–2.2 eV band gap of Cu 2 O. However, existing ECD-Cu 2 O devices are plagued by poor crystallinity and low selectivity of the electron and hole transport layers. Here we use Vibrating Kelvin Probe Surface Photovoltage Spectroscopy (VKP-SPV) to probe the charge transfer selectivity in FTO/ZnO/Cu 2 O/PEDOT:PSS/Ni heterojunction solar cells. Selective electron extraction is achieved at the ZnO back contact to Cu 2 O, as confirmed by a negative surface photovoltage signal. While the uncoated Cu 2 O surface is electron-selective due to the formation of a hole depletion layer, spin coating of a PEDOT:PSS film turns it into a hole-selective interface. After adding nickel metal ink top electrodes, functional 1.0 cm 2 solar cells with power conversion efficiency (PCE) of up to 0.07%, 195 mV open-circuit voltage, and 1.28 mA cm –2 short-circuit photocurrent are achieved. The photovoltaic performance is higher for aluminum doped zinc oxide (AZO) substrates than for fluorine doped tin oxide (FTO) due to the presence of a n-/p-junction that further increases the electron selectivity of the AZO/ZnO/Cu 2 O contacts. Overall, this work demonstrates the first application of PEDOT:PSS as a hole transport layer (HTL) for Cu 2 O and the use of VKP-SPV to measure the photovoltage contributions of the Cu 2 O interfaces. Furthermore, the ability to fabricate Cu 2 O solar cells at near room temperature without the use of vacuum methods or rare elements is an important step towards a scalable Cu 2 O PV technology.

14 SOLAR ENERGY↗

Optimizers for stabilizing likelihood-free inference

A growing number of applications in particle physics and beyond use neural networks as unbinned likelihood ratio estimators applied to real or simulated data. Precision requirements on the inference tasks demand a high-level of stability from these networks, which are affected by the stochastic nature of training. We show how physics concepts can be used to stabilize network training through a physics-inspired optimizer. In particular, the energy conserving descent (ECD) optimization framework uses classical Hamiltonian dynamics on the space of network parameters to reduce the dependence on the initial conditions while also stabilizing the result near the minimum of the loss function. We develop a version of this optimizer known as , which has few free hyperparameters with limited ranges guided by physical reasoning. We apply to representative likelihood-ratio estimation tasks in particle physics and find on average that it out-performs the widely used Adam optimizer. We expect that ECD will be a useful tool for wide array of data-limited problems, where it is computationally expensive to exhaustively optimize hyperparameters and mitigate fluctuations with ensembling.

Monte Carlo methods↗

Non-Invasive Functional-Brain-Imaging with an OPM-based Magnetoencephalography System

A non-invasive functional-brain-imaging system based on optically-pumped-magnetometers (OPM) is presented. The OPM-based magnetoencephalography (MEG) system features 20 OPM channels conforming to the subject’s scalp. We have conducted two MEG experiments on three subjects: assessment of somatosensory evoked magnetic field (SEF) and auditory evoked magnetic field (AEF) using our OPM-based MEG system and a commercial MEG system based on superconducting quantum interference devices (SQUIDs). We cross validated the robustness of our system by calculating the distance between the location of the equivalent current dipole (ECD) yielded by our OPM-based MEG system and the ECD location calculated by the commercial SQUID-based MEG system. We achieved sub-centimeter accuracy for both SEF and AEF responses in all three subjects. Due to the proximity (12 mm) of the OPM channels to the scalp, it is anticipated that future OPM-based MEG systems will offer enhanced spatial resolution as they will capture finer spatial features compared to traditional MEG systems employing SQUIDs.

60 APPLIED LIFE SCIENCES↗

Qudit Gate Decomposition Dependence for Lattice Gauge Theories

In this work, we investigate the effect of decomposition basis on primitive qudit gates on superconducting radio-frequency cavity-based quantum computers with applications to lattice gauge theory. Three approaches are tested: SNAP & Displacement gates, ECD & single-qubit rotations $R(\theta,\phi)$, and optimal pulse control. For all three decompositions, implementing the necessary sequence of rotations concurrently rather then sequentially can reduce the primitive gate run time. The number of blocks required for the faster ECD &$R_p(\theta)$ is found to scale $\mathcal{O}(d^2)$, while slower SNAP & Displacement set scales at worst $\mathcal{O}(d)$. For qudits with $d<10$, the resulting gate times for the decompositions is similar, but strongly-dependent on experimental design choices. Optimal control can outperforms both decompositions for small $d$ by a factor of 2-12 at the cost of higher classical resources. Lastly, we find that SNAP & Displacement are slightly more robust to a simplified noise model.

Kürkçüoglu, Doga Murat↗

Can magnetogenesis driven by dynamo instabilities in chiral fermion plasmas, favor Einstein–Cartan AdS cosmology?

In this letter we show that the magnetic field (MF) bounds induced by Einstein–Cartan–de Sitter (EC) with AdS anti-de Sitter spacetime geometry and fermionic torsion with chiral dynamo plasmas instabilities, with inhomogeneous uniform chiral chemical potential, indicates that there is a possibility, as far as magnetogenesis is concerned, that we may obtain more stringent results within ECAdS gravity, compared with general relativity (GR) limits obtained by Tsagas using torsionless magnetogenesis. Spinorial fermionic source with torsion induces a chiral plasmas oscillation. The time dependent chiral chemical potential, sometimes associated formally with torsion, (de Andrade, 2018), is obtained from chiral flipping equation. The MFs obtained from the present universe ECdS chiral dynamo model, meet the criteria of galactic seed fields with better limits within Tsagas range (Tsagas, 2015) seed galactic magnetic fields for dynamo mechanisms, than the bound obtained by chiral dynamos in torsionless AdS cosmology. Majorana neutrinos are used as spatial components of axial spin-torsion source of dynamo instability from neutrino asymmetry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Deep eutectic solvents as green and sustainable diluents in headspace gas chromatography for the determination of trace level genotoxic impurities in pharmaceuticals

Genotoxic impurities (GTIs) are potential carcinogens that need to be controlled down to ppm or lower concentration levels in pharmaceuticals under strict regulations. The static headspace gas chromatography (HS-GC) coupled with electron capture detection (ECD) is an effective approach to monitor halogenated and nitroaromatic genotoxins. Deep eutectic solvents (DESs) possess tunable physico-chemical properties and low vapor pressure for HS-GC methods. In this study, zwitterionic and non-ionic DESs have been used for the first time to develop and validate a sensitive analytical method for the analysis of 24 genotoxins at sub-ppm concentrations. Compared to non-ionic diluents, zwitterionic DESs produced exceptional analytical performance and the betaine: 7 (1,4- butane diol) DES outperformed the betaine: 5 (1,4-butane diol) DES. Limits of detection (LOD) down to the 5-ppb concentration level were achieved in DESs. Wide linear ranges spanning over 5 orders of magnitude (0.005–100 µg g –1 ) were obtained for most analytes with exceptional sensitivities and high precision. The method accuracy and precision were validated using 3 commercially available drug substances and excellent recoveries were obtained. Finally, this study broadens the applicability of HS-GC in the determination of less volatile GTIs by establishing DESs as viable diluent substitutes for organic solvents in routine pharmaceutical analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

Chemical, physical, biological and materials engineering disciplines use a variety of chiroptical spectroscopies to probe geometrical and optical asymmetry in molecules and particles. Electronic (ECD) and vibrational (VCD) circular dichroism are the most common of these techniques and collectively enable the studies of electronic and vibronic transitions with energies between 0.1 and 5.0 eV. The vibrational states with characteristic energies in the range of 0.001–0.01 eV carry valuable information about concerted intermolecular motions in molecules and crystals involving multiple atoms. These vibronic transitions located in the terahertz (THz) part of the spectrum become increasingly more important for the chemistry, physics, and biology of complex molecules and materials However, the methodology and hardware of THz circular dichroism (TCD) are much less developed than the chiroptical spectroscopies for ultraviolet, visible, near- and mid infrared photons. In this report we provide theoretical foundations, practical implementations, comparative assessments, and exemplary applications of TCD spectroscopy. We show that the sign, intensity, and position of TCD peaks are highly sensitive to the three-dimensional structure and long-range organization of molecular crystals, which offer unique capabilities to study (bio) molecules, their crystals, and nanoscale assemblies and apply the novel data processing methodologies. TCD also offers a convenient toolbox to identify new physical phenomena, such as chiral phonons and their propagation in nanostructured matter. We also discuss the major challenges, emerging opportunities and promising research directions, including broad investigation of chiral phonons observed in chiral (nano) crystals and emerging machine learning methodologies for TCD in biological and nanoscale structures. Ubiquity of low-frequency vibrations with rotational components in biomolecular structures, combined with sharpness of peaks in TCD spectra, enables a variety of technological translations.

36 MATERIALS SCIENCE↗

Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein

Diverse extracellular proteins negatively regulate WNT signaling. One such regulator is adenomatosis polyposis coli down-regulated 1 (APCDD1), a conserved single-span transmembrane protein. In response to WNT signaling in a variety of tissues, APCDD1 transcripts are highly up-regulated. We have determined the three-dimensional structure of the extracellular domain of APCDD1, and this structure reveals an unusual architecture consisting of two closely apposed β-barrel domains (ABD1 and ABD2). ABD2, but not ABD1, has a large hydrophobic pocket that accommodates a bound lipid. The APCDD1 ECD can also bind to WNT7A, presumably via its covalently bound palmitoleate, a modification that is common to all WNTs and is essential for signaling. This work suggests that APCDD1 functions as a negative feedback regulator by titrating WNT ligands at the surface of responding cells.

59 BASIC BIOLOGICAL SCIENCES↗

Circuit QED Pulse Control Interface

The Circuit Quantum Electrodynamics (Circuit QED) Pulse Control Interface provides a robust platform for designing and testing control signals in transmon-cavity systems. Utilizing a PyQt5-based drag-and-drop GUI, this tool facilitates the implementation of two key protocols: Selective Number-dependent Arbitrary Phase (SNAP)-Displacement and Echoed Conditional Displacement (ECD). It offers real-time pulse visualization and supports CSV exports and imports for integrating custom signals, thereby enhancing circuit QED experimental workflows. Simulations performed using QuTiP confirm the high fidelity of quantum state preparations and the effectiveness of the implemented controls. Future developments will focus on interfacing the tool with hardware and enhancing signal generation accuracy.

Lin, Yuqing↗

Building a Long-Lived 3D Multimode Quantum Processing Unit with TESLA Cavities

Superconducting radio-frequency (SRF) cavities, such as TESLA-shaped cavities, are excellent candidates for long-lived quantum memories. Integrating these cavities with nonlinear elements, such as transmons, enables universal quantum control; however, this integration can often introduce unwanted losses. In this talk, we present the successful integration of a long-lived 2-cell TESLA cavity with an ancillary qubit, forming a quantum processing unit (QPU) that allows for robust control while maintaining coherence. We demonstrate universal control of the QPU through various schemes, including ancilla-cavity sideband and echoed conditional displacement (ECD) methods, enabling fault-tolerant high-fidelity preparation of large Fock states and fast entanglement generation. These results illustrate the versatility and efficiency of our 3D quantum processing unit, paving the way for advanced quantum computing applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

De novo synthesis and near atomic resolution imaging of host immune receptors critical for pathogen recognition (Abbreviated Final Report)

The innate immune system serves as the body’s first line of defense against invading pathogens, responding rapidly through the deployment of immune cells at common sites of infection, such as the skin and airways. These immune-cell sentinels express a range of highly conserved receptors, including Toll-like receptors (TLRs), which recognize and bind to pathogen-derived components. This recognition event triggers intracellular signaling cascades that initiate and coordinate immune responses. Despite their significance, the complete structural characterization of full-length TLRs, including their extracellular domain (ECD), transmembrane domain (TMD), and Toll/interleukin-1 receptor (TIR) domain, remains incomplete. In this study, we examined the expression and isolation of human TLR4 incorporated into nanodiscs using two approaches: a cell-free synthesis system and a cell-based transfection strategy employing Expi293F cells derived from the human embryonic kidney lineage. Our findings demonstrate that NLP-bound human TLR4 produced via the cell-based method yielded functional protein suitable for time-resolved single-particle cryo-electron microscopy (cryo-EM). This advancement enables structural characterization of full-length TLR4, maintaining the integrity of its extracellular domain, transmembrane domain, and Toll/Interleukin-1 receptor (TIR) domain.

59 BASIC BIOLOGICAL SCIENCES↗

Aculeaxanthones A–E, new xanthones from the marine-derived fungus Aspergillus aculeatinus WHUF0198

Introduction Dimeric natural products are widespread in plants and microorganisms, which usually have complex structures and exhibit greater bioactivities than their corresponding monomers. In this study, we report five new dimeric tetrahydroxanthones, aculeaxanthones A−E ( 4−8 ), along with the homodimeric tetrahydroxanthone secalonic acid D ( 1 ), chrysoxanthones B and C ( 2 and 3 ), and 4−4’-secalonic acid D ( 9 ), from different fermentation batches of the title fungus. Methods A part of the culture was added to a total of 60 flasks containing 300 ml each of number II fungus liquid medium and culture 4 weeks in a static state at 28˚C. The liquid phase (18 L) and mycelia was separated from the fungal culture by filtering. A crude extract was obtained from the mycelia by ultrasound using acetone. To obtain a dry extract (18 g), the liquid phase combined with the crude extract were further extracted by EtOAc and concentrated in vacuo. The MIC of anaerobic bacteria was examined by a broth microdilution assay. To obtain MICs for aerobic bacteria, the agar dilution streak method recommended in Clinical and Laboratory Standards Institute document (CLSI) M07-A10 was used. Compounds 1−9 was tested against the Bel-7402, A-549 and HCT-116 cell lines according to MTT assay. Results and Discussion The structures of these compounds were elucidated on the base of 1D and 2D NMR and HR-ESIMS data, and the absolute configurations of the new xanthones 4−8 were determined by conformational analysis and time-dependent density functional theory-electronic circular dichroism (TDDFT-ECD) calculations. Compounds 1–9 were tested for cytotoxicity against the Bel-7402, A549, and HCT-116 cancer cell lines. Of the dimeric tetrahydroxanthone derivatives, only compound 6 provided cytotoxicity effect against Bel-7402 cell line (IC50, 1.96 µM). Additionally, antimicrobial activity was evaluated for all dimeric tetrahydroxanthones, including four Gram-positive bacteria including Enterococcus faecium ATCC 19434, Bacillus subtilis 168, Staphylococcus aureus ATCC 25923 and MRSA USA300; four Gram-negative bacteria, including Helicobacter pylori 129, G27, as well as 26,695, and multi drug-resistant strain H. pylori 159, and one Mycobacterium M. smegmatis ATCC 607. However, only compound 1 performed activities against H. pylori G27, H. pylori 26695, H. pylori 129, H. pylori 159, S. aureus USA300, and B. subtilis 168 with MIC values of 4.0, 4.0, 2.0, 2.0, 2.0 and 1.0 μg/mL, respectively.

Wu, Jun↗

VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments

An open-source program named VeloxChem has been developed for the calculation of electronic real and complex linear response functions at the levels of Hartree–Fock and Kohn–Sham density functional theories. With an object-oriented program structure written in a Python/C++ layered fashion, VeloxChem enables time-efficient prototyping of novel scientific approaches without sacrificing computational efficiency, so that molecular systems involving up to and beyond 500 second-row atoms (or some 10,000 contracted and in part diffuse Gaussian basis functions) can be routinely addressed. In addition, VeloxChem is equipped with a polarizable embedding scheme for the treatment of the classical electrostatic interactions with an environment that in turn is modeled by atomic site charges and polarizabilities. The underlying hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme makes VeloxChem suitable for execution in high-performance computing cluster environments, showing even slightly beyond linear scaling for the Fock matrix construction with use of up to 16,384 central processing unit (CPU) cores. An efficient—with respect to convergence rate and overall computational cost—multifrequency/gradient complex linear response equation solver enables calculations not only of conventional spectra, such as visible/ultraviolet/X-ray electronic absorption and circular dichroism spectra, but also time-resolved linear response signals as due to ultra-short weak laser pulses.

97 MATHEMATICS AND COMPUTING↗