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At least 91 records · Page 5

Optical Control of Dopamine D2-like Receptors with Cell-Specific Fast-Relaxing Photoswitches

Dopamine D2-like receptors (D2R, D3R, and D4R) control diverse physiological and behavioral functions and are important targets for the treatment of a variety of neuropsychiatric disorders. Their complex distribution and activation kinetics in the brain make it difficult to target specific receptor populations with sufficient precision. We describe a new toolkit of light-activatable, fast-relaxing, covalently taggable chemical photoswitches that fully activate, partially activate, or block D2-like receptors. This technology combines the spatiotemporal precision of a photoswitchable ligand (P) with cell type and spatial specificity of a genetically encoded membrane anchoring protein (M) to which the P tethers. These tools set the stage for targeting endogenous D2-like receptor signaling with molecular, cellular, and spatiotemporal precision using only one wavelength of light.

59 BASIC BIOLOGICAL SCIENCES↗

The cosmic DANCe of Perseus

Context. Star-forming regions are excellent benchmarks for testing and validating theories of star formation and stellar evolution. The Perseus star-forming region, being one of the youngest (< 10 Myr), closest (280-320 pc), and most studied in the literature, is a fundamental benchmark. Aims. We aim to study the membership, phase-space structure, mass, and energy (kinetic plus potential) distribution of the Perseus star-forming region using public catalogues (Gaia, APOGEE, 2MASS, and Pan-STARRS). Methods. We used Bayesian methodologies that account for extinction to identify the Perseus physical groups in the phase-space, retrieve their candidate members, derive their properties (age, mass, 3D positions, 3D velocities, and energy), and attempt to reconstruct their origin. Results. We identify 1052 candidate members in seven physical groups (one of them new) with ages between 3 and 10 Myr, dynamical super-virial states, and large fractions of energetically unbounded stars. Their mass distributions are broadly compatible with that of Chabrier for masses ≳0.1 M ⊙ and do not show hints of over-abundance of low-mass stars in NGC 1333 with respect to IC 348. These groups’ ages, spatial structure, and kinematics are compatible with at least three generations of stars. Future work is still needed to clarify if the formation of the youngest was triggered by the oldest. Conclusions. The exquisite Gaia data complemented with public archives and mined with comprehensive Bayesian methodologies allow us to identify 31% more members than previous studies, discover a new physical group (Gorgophone: 7 Myr, 191 members, and 145 M ⊙ ), and confirm that the spatial, kinematic, and energy distributions of these groups support the hierarchical star formation scenario.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Impact of atomic substitution on core-hole relaxation dynamics: A study of Br 2 and IBr

Understanding inner-shell decay processes in heavy-element molecules is essential for unraveling x-ray-induced photodynamics and advancing molecular imaging techniques. Here, in this study, we investigate the influence of atomic substitution on core-hole relaxation dynamics and molecular fragmentation in Br 2 and IBr, initiated by x-ray ionization absorption at the Br K-edge. Using a combination of x-ray/ion coincidence measurements and Monte Carlo/molecular dynamics simulations, we track the charge distribution and the kinetic energy release (KER) of fragment ions with a total charge from 2+ to 8+. For both molecules, the simulated KER values show good agreement with experiment across different fragmentation channels. Our comparison reveals that substituting Br with the heavier I atom in IBr has a minimal impact on the inner-shell electronic decay process but significantly influences nuclear motion, leading to slower dissociation and thus a KER close to the Coulomb limit—an effect attributed to the atomic mass. These findings highlight the interplay between electronic and nuclear effects in molecular fragmentation, particularly in heavy-element species, and provide new insights into medical therapies, structural biology, and astrophysics.

Bhat, Nivedita [Argonne National Laboratory (ANL),↗

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Two-body dissociation of formic acid following double ionization by ultrafast laser pulses

We studied the fragmentation of planar formic acid (HCOOH) molecules following their double ionization by intense ultrashort laser pulses. Deuterium tagging (i.e., HCOOD) combined with coincidence momentum imaging measurements of all fragment ions enabled determination of the role of the hydroxyl and carboxyl hydrogen atoms in the breakup. Specifically, we observe a strong preference for the hydroxyl (OD) group to remain intact in a ${\mathrm{HCOOD}}^{2+}{\rightarrow}{\mathrm{OD}}^{+}+{\mathrm{HCO}}^{+}$ fragmentation, which is an order of magnitude more likely than ${\mathrm{OH}}^{+}+{\mathrm{DCO}}^{+}$. An even larger preference for breaking the H-C bond over the O-H bond is observed in the ${\mathrm{H}}^{+}+{\mathrm{DCO}}_{2}^{+}$ and ${\mathrm{D}}^{+}+{\mathrm{HCO}}_{2}^{+}$ deprotonation channels. Bond rearrangement, leading to ${\mathrm{H}}_{2}^{+}$ or ${\mathrm{H}}_{2}{\mathrm{O}}^{+}$ formation, exhibits no isotopic preference. The kinetic-energy-release distributions of the ${\mathrm{OH}}^{+}+{\mathrm{DCO}}^{+}$ and ${\mathrm{O}}^{+}+{\mathrm{H}}_{2}{\mathrm{CO}}^{+}$ breakup channels suggest that more than one process contributes to these final products, although further theoretical work is needed to identify the specific paths.

74 ATOMIC AND MOLECULAR PHYSICS↗

Kinetic-energy dissipation and fluctuations in strongly damped heavy-ion collisions within the stochastic mean-field approach

Microscopic mean-field approaches have been successful in describing the most probable reaction outcomes in low-energy heavy-ion reactions. However, those approaches are known to severely underestimate dispersions of observables around the average values that has limited their applicability. Recently it has been shown that a quantal transport approach based on the stochastic mean-field (SMF) theory significantly improves the description, while its application has been limited so far to fragment mass and charge dispersions. In this work, we extend the quantal transport approach based on the SMF theory for relative kinetic energy dissipation and angular momentum transfer in low-energy heavy-ion reactions. Based on the SMF concept, analytical expressions are derived for the radial and tangential friction and associated diffusion coefficients. Those quantal transport coefficients are calculated microscopically in terms of single-particle orbitals within the time-dependent Hartree-Fock (TDHF) approach. As the first application of the proposed formalism, we consider the radial linear momentum dispersion, neglecting the coupling between radial and angular momenta. We analyze the total kinetic energy (TKE) distribution of binary reaction products in the 136 Xe + 208 Pb reaction at E c.m. =526 MeV and compare with experimental data. From time evolution of single-particle orbitals in TDHF, the radial diffusion coefficient is computed on a microscopic basis, while a phenomenological treatment is introduced for the radial friction coefficient. By solving the quantal diffusion equation for the radial linear momentum, the dispersion of the radial linear momentum is obtained, from which one can construct the TKE distribution. We find that the calculations provide a good description of the TKE distribution for strongly damped events with large energy losses, TKEL ≳ 150 MeV. However, the calculations underestimate the TKE distribution for smaller energy losses. Further studies are needed to improve the technical details of calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Diversifying self-assembled phases in block copolymer thin films via blending

Block copolymer (BCP) thin films readily self-assemble into intricate nanoscale morphologies, with structure dictated by chain architecture. As the field searches for more control over structure formation, it is natural to investigate more sophisticated control mechanisms, such as synthesizing more complex chain architectures or applying directing fields. We review the use of a simple but powerful method for controlling self-assembly: blending of BCPs with homopolymers or other BCPs. Blending enables tailoring ordering kinetics, the spatial distribution of chains throughout the film thickness, and the nanoscale morphology itself. Blending is thus emerging as a remarkably simple and powerful means of tailoring self-assembled morphologies.

36 MATERIALS SCIENCE↗

Calculated fission-fragment mass yields and average total kinetic energies of heavy and superheavy nuclei

Fission-fragment mass and total-kinetic-energy (TKE) distributions following fission of even-even nuclides in the region \(74 \le Z \le 126\) and \(92 \le N \le 230\) , comprising 896 nuclides have been calculated using the Brownian shape-motion method. The emphasis is the region of superheavy nuclei. To show compatibility with earlier results the calculations are extended to include earlier studied regions. An island of asymmetric fission is obtained in the superheavy region, \(106\le Z\le 114\) and \(162\le N\le 176\) , where the heavy fragment is found to be close to \(^{208}\) Pb and the light fragment adjusts accordingly. Most experimentally observed \(\alpha \) -decay chains of superheavy nuclei with \(Z > 113 \) terminate by spontaneous fission in our predicted region of asymmetric fission. In these cases, the pronounced large asymmetry is accompanied by a low TKE value compatible with measurements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Finite Element Modeling of Electrochemical Polishing of Niobium in Hydrofluoric-Sulfuric Acid Electrolyte

Niobium (Nb) used in superconducting radio-frequency cavities requires smooth surface to achieve optimal performance. In this work, a finite element model that coupled electrochemistry, heat transfer, and fluid dynamics was developed to investigate the electrochemical polishing mechanisms of Nb, using experimentally measured polarization results of coupon samples as validations. The current and potential distribution, oxide growth kinetics of Nb in a complex cavity geometry was investigated as a function of temperature and coolant flow. A low temperature coolant with intermediate flow rate was found to reduce surface current and ensure oxide uniformity. These results could shed light on the design of future particle accelerators.

SRF accelerator cavity↗

The OCEAN ICE mooring compilation: a standardised, pan-Antarctic database of ocean hydrography and current time series

Continuous moored time series of temperature, salinity, pressure and current speed and direction are of great importance for understanding the continental shelf and under-ice-shelf dynamics and thermodynamics that govern water mass transformations and ice melting in and around Antarctic marginal seas. In these regions, icebergs and sea ice make ship-based mooring deployment and recovery challenging. Nevertheless, over decades, expeditions around the fringe of Antarctica sporadically deployed and recovered hundreds of moored instruments, including those facilitated through ice shelves boreholes. These datasets tend to be archived in a wide range of data centres, with, to our knowledge, no clear format standardisation. As a result, systematic analysis of historical mooring time series in the marginal seas is often challenging. Here we present the first version of a standardised pan-Antarctic moored hydrography and current time series compilation, with broad international contributions from data centres, research institutes and individual data owners. The mooring records in this compilation span over five decades, from the 1970s to the 2020s, providing an opportunity for a systematic study of the pan-Antarctic water mass transport and shelf connectivity. As a demonstration of the utility of this compilation, we present spectral analysis of the compiled current velocity time series, which unsurprisingly shows the dominating presence of tidal variability within most records. This component of the variability is fitted using multi-linear regression to tidal frequencies, and the tidal fit is removed from the original time series to leave de-tided variability. Given the limited record durations to months to years, de-tided variability is dominated by synoptic (3–10 d period), intraseasonal (10–80 d) and seasonal (∼6 months–1 year) signals. The spatial distribution of the kinetic energy integrated within frequency bands is presented and discussed within respective regional contexts, and future avenues of research are proposed. This data compilation is assembled under the endorsement of Ocean-Cryosphere Exchanges in ANtarctica: Impacts on Climate and the Earth System (OCEAN ICE) project (https://ocean-ice.eu/, last access: 23 October 2025) funded by the European Commission and UK Research and Innovation. It is available and regularly updated in NetCDF format with the SEANOE database at https://doi.org/10.17882/99922 (Zhou et al., 2024a).

54 ENVIRONMENTAL SCIENCES↗

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇌ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. In this work, we have studied a single-domain bilin-binding photoreceptor All2699g1 ( Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (P r ) and far red-absorbing (P fr ) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the P r form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ~300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

59 BASIC BIOLOGICAL SCIENCES↗

Verification of an improved equation-free projective integration method for neoclassical plasma-profile evolution in tokamak geometry

A brute-force, long-time gyrokinetic simulation of plasma profile evolution in magnetic fusion devices is not desirable due to large computational resource requirements and a possible accumulation of numerical error. The equation-free projective integration method of Keverekidis et al. [Commun. Math. Sci. 1(4), 715–762 (2003)] is one of the outstanding candidates in projecting micro-scale simulations to a longer timescale. However, its application to tokamak plasma has not been fruitful due to the appearance of spurious transient oscillations in the lifting process, which are present when the kinetic simulations are initialized with a simplified model distribution function and which make the kinetic simulations to deviate from the desired paths. In this work, a kinetically informed lifting algorithm is added to the equation-free projective integration method, which is then verified in the electrostatic gyrokinetic particle-in-cell code XGCa [R. Hager and C. S. Chang, Phys. Plasmas 23, 042503 (2016)] for a neoclassical ion heat transport problem with adiabatic electrons. This new lifting operator is demonstrated to control spurious transients, enabling an over four-times reduction in the overall computing time in the time-evolution of the ion temperature profile in an axisymmetric toroidal plasma. Further reduction in the computing time is found to be limited due to the stability properties of the linear least squares projective integrator.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Explosive Soot Challenge (Final Report)

This project assembled a broad ensemble of modeling and experimentation tools to study the morphological and optical properties of detonation soots in explosive fireballs. A gram-scale hemispherical high explosive was studied in a low-pressure controlled environment using in-situ experimentation with diffusely illuminated visible absorption spectroscopy, particle sizing through light scattering techniques, and post-test collections with subsequent morphological analysis. Hydrocode modeling was performed to replicate the detonation flow observations, and subsequent aerosol kinetics models provided particle size distributions and extinction coefficients from the hydrocode results. Experimentally observed soot morphologies agreed with expectation from the literature - a bimodal distribution was found, brought upon by the particles growing to a size where their inertia and fluid wakes are non-negligible. The aerosol kinetics model did not replicate the observed bimodal size distribution for lack of a coagulation kernel to represent the behavior. To recover particulate optical properties, a spectrally resolved absorption spectroscopy method termed Spectral diffuse back-illuminated extinction imaging (SBI-EI) was developed and implemented on two explosive types. Inverting the absorption spectra using a Kramers-Kronig consistent method yielded the complex index of refraction for the soots produced by the explosives. This method resulted in an unrealistic index of refraction for one of the two explosives, and this is suspected to be due to the model neglecting scattering brought upon by the large particle sizes observed. In addition to the core work, three additional studies were performed in parallel. These investigated the impact of scattering on diffuse absorption spectroscopy, studied how soots oxidate and sublimate in a well-controlled shock tube, and laid the theoretical groundwork for a new collision kernel to replicate the bimodal size distribution from the observations. Summaries of these efforts are included at the end of this report.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Fission with Exotic Nuclei (Abbreviated Report)

Nuclear fission is a key mechanism involved in the synthesis of heavy elements in the Cosmos and is the primary explanation for the stability of superheavy elements. Nevertheless, our knowledge of fission remains extremely fragmented. Most experiments have been conducted only on a tiny number of stable actinide nuclei and are often incomplete, leading to gaps in our basic understanding of the process. For many radioactive isotopes, basic fission data such as the charge or mass distribution of the fragments is unknown. These gaps cannot always be filled by simulation alone. Common fission models contain too many free parameters and lack predictive power. In contrast, the fundamental theory of fission under development at LLNL is much more predictive, but its current computational cost is too high to be used extensively for data evaluations. A unique window of opportunity to resolve these limitations has recently opened: the U.S. nuclear science community is ramping up major experimental programs at the Facility for Rare Isotope Beams (FRIB, the DOE flagship facility in low-energy nuclear science), and techniques from machine learning have shown great potential to simplify the use of a fundamental, quantum-mechanical theory of fission. This project has two components. On the experimental side, we acquired and deployed at the HIGS facility a new dual Frisch-Grid ionization chamber to measure correlated fragment-mass, kinetic energy, and angular distributions of fission fragments from induced fission. This new device was used to perform measurements of charge, mass and total kinetic energy of fission fragments in the photofission of 238 U and eight gamma-ray beam energies between 6.2 and 13 MeV, which allowed extracting high-precision independent yields for this reaction. The device was also used to perform measurements of the same quantities in the neutron-induced fission of 234 U with monoenergetic beams of energy between 5 and 8 MeV. In parallel, we collaborated with a team at Commissariat à l’énergie atomique et aux énergies alternatives (CEA) to perform a series of measurements of fission yields in inverse kinematics for the two isotopes of 236 U and 240 Pu. The experiment took place at the Grand Accélérateur National d’Ions Lourds in France in June 2023. The deployment of the VAMOS spectrometer with a new array called PISTA allowed determining the excitation energy of the fissioning system within 1 Mega-electronvolts. The second component of the project involved using deep neural networks to build fast and reliable emulators of our current fission models. In an invited paper published in Frontier in Physics, we showed that autoencoders could successfully compress nuclear wavefunctions in nuclear density functional theory. We achieved a dimensionality reduction of the order of two orders of magnitude while keeping the error in the total energy to less than 0.01%. In a second paper submitted to Physical Review Letters in June 2023 with our collaborators at CEA, we showed that variational autoencoders can learn the collective degrees of freedom driving the fission process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Multiscale Modeling of Nanoparticle Precipitation in Oxide Dispersion-Strengthened Steels Produced by Laser Powder Bed Fusion

Laser Powder Bed Fusion (LPBF) enables the efficient production of near-net-shape oxide dispersion-strengthened (ODS) alloys, which possess superior mechanical properties due to oxide nanoparticles (e.g., yttrium oxide, Y-O, and yttrium-titanium oxide, Y-Ti-O) embedded in the alloy matrix. To better understand the precipitation mechanisms of the oxide nanoparticles and predict their size distribution under LPBF conditions, we developed an innovative physics-based multiscale modeling strategy that incorporates multiple computational approaches. These include a finite volume method model (Flow3D) to analyze the temperature field and cooling rate of the melt pool during the LPBF process, a density functional theory model to calculate the binding energy of Y-O particles and the temperature-dependent diffusivities of Y and O in molten 316L stainless steel (SS), and a cluster dynamics model to evaluate the kinetic evolution and size distribution of Y-O nanoparticles in as-fabricated 316L SS ODS alloys. The model-predicted particle sizes exhibit good agreement with experimental measurements across various LPBF process parameters, i.e., laser power (110–220 W) and scanning speed (150–900 mm/s), demonstrating the reliability and predictive power of the modeling approach. The multiscale approach can be used to guide the future design of experimental process parameters to control oxide nanoparticle characteristics in LPBF-manufactured ODS alloys. Additionally, our approach introduces a novel strategy for understanding and modeling the thermodynamics and kinetics of precipitation in high-temperature systems, particularly molten alloys.

Wang, Zhengming (ORCID:0000000241627112)↗

Stability of superthermal strahl electrons in the solar wind

We present a kinetic stability analysis of the solar wind electron distribution function consisting of the Maxwellian core and the magnetic-field aligned strahl, a superthermal electron beam propagating away from the sun. We use an electron strahl distribution function obtained as a solution of a weakly collisional drift-kinetic equation, representative of a strahl affected by Coulomb collisions but unadulterated by possible broadening from turbulence. This distribution function is essentially non-Maxwellian and varies with the heliospheric distance. The stability analysis is performed with the Vlasov–Maxwell linear solver leopard. We find that depending on the heliospheric distance, the core-strahl electron distribution becomes unstable with respect to sunward-propagating kinetic-Alfvén, magnetosonic, and whistler modes, in a broad range of propagation angles. The wavenumbers of the unstable modes are close to the ion inertial scales, and the radial distances at which the instabilities first appear are on the order of 1 au. However, we have not detected any instabilities driven by resonant wave interactions with the superthermal strahl electrons. Instead, the observed instabilities are triggered by a relative drift between the electron and ion cores necessary to maintain zero electric current in the solar wind frame (ion frame). Contrary to strahl distributions modelled by shifted Maxwellians, the electron strahl obtained as a solution of the kinetic equation is stable. Our results are consistent with the previous studies based on a more restricted solution for the electron strahl.

79 ASTRONOMY AND ASTROPHYSICS↗

Elucidating the Impact of Cis – Trans Organic Structure Directing Agent Isomer Ratios on the Aluminum Distribution Within SSZ-39

Despite their widespread use, the mechanisms governing the synthesis of zeolite catalysts are still poorly understood. A notable example of this problem is the uncertainty surrounding the influence of synthesis conditions on the placement of Al atoms in the zeolite framework which determines the active sites available for catalytic species. In this work, the role of the cis to trans isomer ratio of the OSDA N,N-dimethyl-3-5-dimethylpiperidinium on the energetics of 26 distinct Al pair distributions in SSZ-39 is examined both in the presence and absence of Na using density functional theory calculations. The initial orientation of the OSDA was found to have a significant impact on the final energies present, necessitating the screening of a large number of initial orientations with force field calculations and single point DFT calculations. Ground state energies were found to vary significantly with the ratio of cis to trans OSDAs with a Boltzmann distribution revealing the most likely Al pair distributions shift from sharing the same 8 membered rings to sharing the same double six membered rings to having no shared subunits as one increases the amount of cis OSDA present within the framework. The presence of Na was found to favor Al pair distributions where both Als occupied the same 6-membered ring. When an implicit solvent model was used to evaluate ground state energies the ideal Na sites shifted from 6-membered rings to empty SSZ-39 cages while OSDA positions and orientations remained largely the same. To provide insight on how kinetic factors may influence Al distributions, formation energies we calculated for connected double six membered rings. Further, these formation energies revealed a preference for Al pairs to occupy the same 4-membered ring which indicates kinetic and thermodynamic control may lead to different Al distributions in SSZ-39.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗