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Understanding, inhibiting, and engineering membrane transporters with high-throughput mutational screens

Promiscuous membrane transporters play vital roles across domains of life, mediating the uptake and efflux of structurally and chemically diverse substrates. Although many transporter structures have been solved, the fundamental rules of polyspecific transport remain inscrutable. In recent years, high-throughput genetic screens have solidified as powerful tools for comprehensive, unbiased measurements of variant function and hypothesis generation, but have had infrequent application and limited impact in the transporter field. In this primer, we describe the principles of high-throughput screening methods available for studying polyspecific transporters and comment on the necessity and potential of high-throughput methods for deciphering these transporters in particular. We present several screening approaches which could provide a fundamental understanding of the molecular basis of function and promiscuity in transporters. Here, we further posit how this knowledge can be leveraged to design inhibitors that combat multidrug resistance and engineer transporters as needed tools for synthetic biology and biotechnology applications.

EPIs

Ion Transport in Carbon Nanotube Porins with a pH-Switchable Entrance Gate

Molecular transport in nanofluidic channels often differs drastically from conventional bulk transport. Strong confinement in those channels amplifies the roles of surface transport, surface defects, and molecular gates. Here, in this study, we introduce a chemical functionality at the nanotube rim that acts as a pH-triggered molecular gate by forming a movable lid that blocks the pore entrance. We use ion and proton transport measurements to show that these sub-1 nm diameter fluorescent ultrashort carbon nanotube porins (FUNPs) modulate ion transport by switching between the “open” and “closed” conformations of this gate. Specifically, at neutral pH the channel lid is open, allowing unimpeded ion transport through the gate, whereas at acidic pH values the lid forms a “closed” conformation that blocks transport through the nanotube. We also report first-principles MD simulations that confirm this gating mechanism and reveal molecular details of the ion and proton transport processes in these functional nanopores.

Carbon nanotubes

COG User's Manual: A Multiparticle Monte Carlo Transport Code (Sixth Edition)

COG is a high-resolution code for the Monte Carlo simulation of coupled particle transport in arbitrary 3-D geometry. COG will transport neutrons, protons, deuterons, alpha particles with energies up to hundreds of GeV, and photons with energy ranges limited by the available cross section sets and physics models. Electrons can be transported via the EGS5 electron transport kernel, electrons can also be transported. The COG code is a significant upgrade from earlier Monte Carlo transport codes and has been written specifically to make it more versatile, accurate, and easy to use. COG has provisions for calculating deep penetration (shielding) problems, criticality problems, and neutron activation problems while retains all of the standard capabilities found in other Monte Carlo transport codes. COG uses high-resolution pointwise cross-section databases and makes no compromises in the transport physics, so that the results of a COG run are limited only by the accuracy of the databases used. COG runs primarily on Linux Operating System workstations with MPICH software installed – currently, Red Hat 7 & 8, Windows 10 (Windows Subsystem for Linux –WSL), Ubuntu 16, 18 & 20, OpenSUSE Leap 15.2, Fedora 32, Apple Power Mac with Intel CPU (with MacPorts installed) workstations, and LLNL LC supercomputer CTS-1 cluster with TOSS 3 are supported.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Editorial: Structure and mechanism of microbial membrane active transporters

Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.

mechanism

TSDC: Transportation Secure Data Center: Real-World Data for Planning, Modeling, and Analysis

The Transportation Secure Data Center is a centralized repository for high-resolution transportation data from hundreds of travel and transit surveys and studies. It makes vital transportation data broadly available to users while preserving the privacy of survey participants. It houses surveys and studies conducted by state departments of transportation, metropolitan planning organizations, transit agencies, cities, and other public agencies. Meanwhile, the Livewire Data Platform empowers research, industry, and academic partners to easily and securely preserve, maintain, share, discover, and gain access to transportation and mobility data. Livewire accommodates a range of datasets, including behavioral, experimental, model, analytical, and raw data at the vehicle, traveler, and system levels. Datasets support mobility research and planning spanning urban science, connected and automated vehicles, fueling and charging infrastructure, mobility decision science, multimodal transportation, vehicle efficiency, and more.

33 ADVANCED PROPULSION SYSTEMS

Explosive Byproduct Gas Transport Through Sorptive Geomedia

Current underground nuclear explosion (UNE) detection strategies rely heavily on atmospheric noble gas sampling of radioxenon. However, discriminating nuclear weapons testing programs from civilian sources is difficult due to highly variable atmospheric radioxenon backgrounds and processes affecting subsurface transport of parent radionuclides. Here, we aim to study the transport of gases produced by subsurface explosions as novel stable signatures for underground nuclear explosion (UNE) monitoring. These gases may be produced in large quantities with distinct molecular ratios, which will be impacted by subsurface transport processes. To demonstrate how ratios of gases produced by explosions can change during transport in geomaterials, we conducted laboratory benchtop experiments on the transport of carbon dioxide (CO 2 ) and hydrogen (H 2 ) gases through variably saturated zeolitic tuff, which is abundant at the historic US testing site. We observed that zeolitic tuff sorbs substantial quantities of CO 2 while allowing H 2 to transport more freely, leading to changes in the molecular ratios of the two gases along the transport pathway. Gas uptake in the dry zeolitic tuff core was 72.3% for CO 2 , compared with 53.4% for xenon and 7.6% for H 2 . The presence of 20% water saturation disrupted the CO 2 sorption process, though to a lesser extent than observed for noble gases, with a 36.7% drop in xenon sorption compared with a 21.9% drop for CO 2 . These results represent the first observations of zeolite sorption altering explosive gas ratios during transport through geomedia relevant to nuclear proliferation monitoring.

54 ENVIRONMENTAL SCIENCES

Statistical distributions for transient transport

Here, this paper introduces the use of statistical distributions based on transport differential equations for clear distinction of transport modes within transient kinetic experiments. More specifically, novel techniques are developed for the transient data obtained through the Temporal Analysis of Products (TAP) reactor and are applicable to experiments where pulse response into a gas flow is used. The methodology allows distinguishing between two domains of diffusion transport in heterogeneous catalytic systems, i.e., Knudsen and non-Knudsen diffusion, using statistical fingerprints, and finding the transition domain. Two distribution parameters were obtained that directly result in coefficients that correspond to the concentration and the rate of transport. Using a linear relationship between the rate and concentration coefficients, Knudsen diffusion is revealed when the rate of transport is constant and non-Knudsen diffusion is confirmed when the rate of transport coefficient is a function of the concentration coefficient. As a result, accurate transport information can be extracted from experimental data even in the presence of comprising instrument drift or noise particularly when analyzing higher pressure pulse responses with complex transport. This enables more direct investigation of experiments influenced by gas-phase reactions.

TAP reactor

Curious cross-field transport effects in multi-ion, magnetized plasma

In contrast to single-ion plasma, multiple-ion-species plasma exhibits new, curious, and large transport effects. On short timescales, where ions exchange momentum, magnetized multi-ion plasma behaves as a most unusual substance, compressible across field lines in number density but incompressible in charge density. It takes 40 times longer for electrons to participate. In this ion–ion cross-field transport regime, we identified the charge-incompressibility heat pump effect, transferring heat both spatially and between species. Curiously, the direction of impurity transport strongly depends on plasma magnetization, characterized by the ratio of light ion gyrofrequency to the collision frequency between light and heavy ion species. The expulsion of heavy ion impurities from a hotspot occurs sufficiently quickly to be observable on MagLIF, so long as plasma becomes sufficiently collisionally magnetized under implosion. Even more curious, multi-ion transport changes its nature in partially ionized plasma, where ions occupy different charge states. In this regime, we identify a partial-ionization deconfinement effect. The combination of cross-field transport, ionization, and recombination leads to a net ion charge moving across magnetic field lines on the ion–ion transport timescale as opposed to the electron–ion transport timescale. Cross-field transport effects in multi-ion plasma are important in a number of applications, including nuclear fusion and plasma mass filters.

Mlodik, M. E. (ORCID:0000000343003941)

Challenges and approaches to interpretive modeling of boundary plasma and neutral transport in a closed, pumped divertor

An experimental discharge from the DIII-D tokamak is modeled using the SOLPS-ITER code suite and compared against measurements in the pumped and relatively closed upper divertor. Uncertainties of boundary plasma simulations are identified by attempting to match code inputs to experimental conditions, including iteratively solving transport coefficients to match upstream experimental profiles using varying quantities of core particle flux, different pumping models, and various assumptions of ion thermal transport. Simulated boundary conditions for particle injection at the core interface are shown to be relevant to the plasma solution at the divertor targets, even if upstream transport is modified so that plasma profiles are comparatively similar, although seperatrix density is not held constant. When upstream plasma profiles are matched to experimental measurements by varying diffusive transport coefficients, using either poloidally symmetric or ballooning structure, the model finds a majority of injected energy being transported radially off the computational domain, in conflict with experimental radiated power measurements and heat flux measurements at the divertor target. Imposing a maximum thermal diffusivity or radially shifting the experimental separatrix location of the fitted profiles to increase power conducted to the targets by increasing the upstream electron temperature does not significantly modify this result. Including a thermalizing plenum volume in the simulation domain is shown to maintain the experimental volumetric pumping rate without knowing the neutral energy distribution incident on the pump duct a priori. By modifying transport parameters to match different assumptions for ion temperature, downstream neutral pressure changes by more than a factor of two, suggesting that attention to ion thermal transport may be a critical parameter for simulations to accurately resolve recycling and neutral transport, particularly in a closed divertor geometry. In addition to quantifying various modeling uncertainties, this work motivates both further experimental study and modeling improvements to improve predictive capabilities.

divertor

Anisotropic Thermal Transport in Quasi-2D Ruddlesden-Popper Hybrid Perovskite Superlattices

Two-dimensional hybrid metal-halide perovskites (2D-MHPs) have emerged as important solution-processed semiconductors with favorable optical and electronic properties for diverse applications in photovoltaics, optoelectronics, and spintronics. The quasi-2D layered structures, featuring large acoustic impedance mismatches between the organic and inorganic sublattices, are expected to result in distinct and anisotropic thermal transport properties along the cross-plane and in-plane directions. Here, we introduce transducer-free vibrational-pump-visible-probe (VPVP) approaches that enable accurate quantification of anisotropic thermal transport properties in various archetypical single-crystalline 2D-MHPs. Specifically, using VPVP spectroscopy and VPVP microscopy, we measure the anisotropic thermal diffusivities of 2D-MHPs with systematically varied Pb-I octahedral layer thicknesses, as well as organic spacer types and lengths, revealing how these structural parameters alter the cross-plane and in-plane thermal transport properties in distinct ways. While diffuse interface scattering plays an important role in dictating cross-plane thermal transport, in-plane thermal transport is primarily determined by phonon transport within interconnected inorganic layers. Density functional theory incorporating four-phonon scatterings provides further insight into the low thermal conductivity and modest thermal conduction anisotropy in 2D-MHPs. Our work demonstrates a new all-optical and noncontact method, which requires minimal sample preparation and allows direct visualization of cross-plane and in-plane thermal transport, potentially compatible with sample environments. The demonstrated VPVP approaches can advance understanding of thermal transport in 2D-MHPs as well as wide-ranging hybrid and polymeric semiconductors beyond 2D-MHPs.

36 MATERIALS SCIENCE

Bubble Mass Transport Measurement in the Large-Scale Test Loops at Oak Ridge National Laboratory

Molten salts are complex fluids that incorporate multi-phase behavior depending on the chemistry and the physical properties of the entrained components. These components include the carrier salt, the actinide fuel, and fission, activation, and corrosion products, the concentrations of which depends on the burnup history of the salt. Radionuclide transport from the salt into the cover gas / off-gas system depends on volatility as predicted by thermochemistry, but data from the Molten Salt Reactor Experiment (MSRE) conducted in the late 1960s suggest that bubble formation and transport are also important. Anomalously high fractions of noble metals were found in the off-gas system and were attributed to transportation with parent salt aerosols and their association with rising noble gas bubbles. The prediction of such phenomena requires coupled neutronic, thermal hydraulic, and chemical equilibrium calculations, the framework of which is being developed within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program supported by the US Department of Energy (DOE) Office of Nuclear Energy (NE). However, separate effects tests and models of experiments using tools such as SAM and Thermochimica can guide model developers through important processes. Conversely, model development guides the choice of experiments and systems to provide data that are relevant for validation. This report describes several experiments that tracked gas transport in molten salts, ranging from small-scale systems to large-scale loops. Gas transportation in a molten salt, LiCl-KCl, has been studied using the shadowgraph technique. Sensors such as residual gas analysis, Raman spectroscopy, and laser-induced breakdown spectroscopy have been tested for off-gas measurements. These data were used to interpret how the gases move through the upstream salt / cover gas and the interface between them. Differential pressure measurements were able to detect individual gas bubbles as they popped at the liquid–gas interface. Salt aerosols were collected on a cascade impactor. Their formation was also observed directly via the shadowgraph method, and most of these aerosols were launched ballistically into the cover gas. Fine mists could also be observed. Convection currents through the salt were visualized and can be used to calculate the thermophysical properties of the salt itself. The apparatuses described in this report and in a previous work (McFarlane et al. 2023) have been commissioned and are available for use in making further measurements of salt/surrogate fission product behavior. Novel approaches using neutron imaging are planned for the study of fluoride salts, which cannot be contained in quartz, so shadowgraph visualization is not available. Bubble transport in convective flow and in a slow-moving salt column are planned. The mobile laser-induced breakdown spectroscopy (LIBS) system is available for several applications, including iodine capture in a molten hydroxide scrubber, H2 transport though molten salts to complement Raman analysis, and online tracking of salt aerosol generation, transport, and deposition. This report summarizes the findings from FY24 and the plans for FY25. The work completes milestone M2AT-24OR0702013 of the DOE-NE Advanced Reactor Technology, Molten Salt Reactor Campaign, DOE-NE-5.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Microreactor Incident-Free Transportation Radiation Dose Assessment

This report, prepared by Pacific Northwest National Laboratory (PNNL) for the U.S. Nuclear Regulatory Commission, provides an estimate of the radiation dose related to the transportation of microreactors following the regulatory limits established in Title 10 of the Code of Federal Regulations (10 CFR) 71.47(b). The transportation of irradiated microreactors poses unique challenges. Microreactors may be challenged to meet the current 10 mrem/hr limit at 2 meters from the vehicle in 10 CFR 71.47(b). The need to modify packaging to be within practical weight and size limits for shipping may limit the amount of shielding that can be applied for a microreactor transportation package design. Operational strategies that would necessitate moving a reactor within a short time after its operating life may result in higher radiation dose rates associated with lower cooling times. This study estimates the radiation dose to maximally exposed individuals (MEIs) under the current regulatory radiation level limit of 10 mrem/hr at 2 meters from the vehicle as well as alternative limits of 10, 50, 100, and 200 mrem/hr at 2 meters from the vehicle. This analysis expands on prior incident free transportation radiation dose assessments conducted for spent nuclear fuel (SNF) and radioactive waste transportation. The key factors analyzed include the microreactor fuel type and burnup, shipment cooling periods, shielding designs integrated into transport packaging, and exposure scenarios for MEIs for highway and rail transport. This report considers additional distances that may be associated with compensatory measures to ensure safe transport conditions under varying radiation dose limits, including enhanced routing measures, escort protocols, vehicle inspections, and operational restrictions.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Multiple Operando Fields Can Identify a Predictive Mass Transport Theory in Electrolytes

An electrolyte transport theory connects its transport properties, evolution of spatiotemporal fields (e.g., concentration), and corresponding macroscopic current and voltage responses. Given this interconnection, the transport properties are typically inferred by analyzing the macroscopic response through the lens of a chosen electrolyte transport theory. Unfortunately, the same macroscopic measurements can be analyzed by using different theories to arrive at seemingly dissimilar properties that are inconsistent with each other. Here, we offer a resolution to this dilemma by analyzing multiple spatiotemporal (i.e., operando) fields for a given electrolyte. We show that predictive transport theory can analyze operando fields to estimate underlying transport properties and subsequently predict another operando field. A theory passing this test identifies meaningful transport properties such that the electrolyte behavior can be accurately predicted over a wide range of excitations, and is critical to property-based electrolyte screening and electrolyte discovery efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Large language models for transportation research: Methodologies, state of the art, and future opportunities

The rapid rise of large language models (LLMs) is transforming transportation research, with significant advancements emerging between 2023 and 2025, a period marked by the inception and swift growth of adopting and adapting LLMs for various transportation applications. Despite these significant advancements, however, a systematic review and synthesis of the existing literature remains lacking. This paper aims to fill this gap by providing a comprehensive review of the methodologies and applications of LLMs in transportation. We explore key applications, including autonomous driving, travel behavior prediction, and general transportation-related queries, alongside LLM methodologies such as zero- or few-shot learning, prompt engineering, and fine-tuning. From the review, critical research gaps are identified. From the methodological perspective, many of the research limitations can be addressed by integrating LLMs with existing tools and refining LLM architectures. From the application perspective, research opportunities for LLMs to address various transportation challenges are also explored. By synthesizing these findings, this review not only presents the state-of-the-art LLM adoption and adaptation in transportation, but also proposes future research directions as well as insights and recommendations for policymakers and practitioners, paving the way for greater LLM-driven research innovations in transportation in the future.

42 ENGINEERING

Probing the Fine Symmetry Breaking in High-Temperature Superconductor Bi 2 Sr 2 CaCu 2 O 8+δ with Angle-Resolved Nonreciprocal Transport

After decades of research, symmetry breaking in high-temperature cuprate superconductors remains a key issue to resolve and is relevant to understanding their exotic quantum phases. In the prototypical cuprate superconductor, Bi 2 Sr 2 CaCu 2 O 8+δ (Bi2212), the possible symmetry breaking has been mostly examined microscopically with scanning tunneling microscopy and photoemission spectroscopy. However, macroscopic evidence and the direct implications for electronic transport have remained elusive. Using superconductivity-enhanced nonreciprocal transport, we report macroscopic evidence of inversion symmetry breaking in Bi2212. While the inversion symmetry breaking is subtle, its effect on nonreciprocal transport is significantly enhanced by the vortex motion during the superconducting transition, leading to a robust manifestation of inversion symmetry breaking in macroscopic transport. Combining angle-resolved nonreciprocal transport and 3D tight-binding model calculations, we derive that the inversion symmetry breaking is due to subtle crystal distortions that give rise to both in-plane and out-of-plane polar axes. Our work not only establishes nonreciprocal transport as a sensitive macroscopic probe to provide electrical transport-based evidence of fine symmetry breaking in Bi2212, but also paves the way for novel device applications such as high-temperature superconducting diodes and superconducting spintronics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Polaron Delocalization and Transport in Doped Graphene Nanoribbon Thin Films

Graphene nanoribbons (GNRs) are quantum-confined π-conjugated monolayer semiconductors with attractive properties for optoelectronic applications. However, the ground- and excited-state properties of charge carriers in GNRs are still poorly understood, particularly with regards to the coupling between charges and the GNR lattice and the degree to which this coupling impacts local and macroscopic charge transport. To address this issue, we systematically correlate carrier density-dependent charge transport with spectroscopic modulations in chemically doped thin films of armchair graphene nanoribbons (9-aGNRs). This study combines Fourier transform infrared (FTIR) and ultraviolet−visible−near-infrared (UV−vis−NIR) spectroscopy with both local and macroscopic conductivity measurements to arrive at a full and self-consistent picture of transport in doped GNR thin films. Using three different molecular p-type dopants (i.e., oxidants), we demonstrate that hole polarons are the dominant quasi-particle determining charge transport in GNRs and that the degree of polaron delocalization depends sensitively on the dopant and the hole density. For all three dopants, the local conductivity probed by microwave spectroscopy substantially exceeds the long-range conductivity obtained by four-point probe measurements. Interestingly, the dopant size substantially influences charge transport at high hole densities. We ascribe this effect to different propensities for forming bipolarons with lower mobilities than polarons. Comparison of GNR transport and spectral properties to other prototypical π-conjugated semiconductors (e.g., semiconducting polymers or carbon nanotubes) benchmark the charge transport properties of GNR thin films for optoelectronic devices and applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Technology Development of a High-Capacity High-Assay Low Enriched Uranium Transportation Concept

This paper discusses the technology development (TD) efforts that led to the development of a High-Capacity High-Assay Low Enriched Uranium Transportation (HALEU) transportation concept. In 2018, the Department of Energy (DOE) Office of Nuclear Technology and Research Development tasked Idaho National Laboratory (INL) to investigate strategies to transport large quantities of HALEU. To complete this task, INL collaborated with Pacific Northwest National Laboratory and Oak Ridge National Laboratory. The project was completed in 2020, and one of the project outcomes was a transportation concept that consisting of five individual Type B packages transported on a single legal-weight truck (LWT). The total payload capacity of this concept is 1,881 kg (4,149 lb) of HALEU in the form of uranium dioxide (UO2) powder. The concept utilizes an existing Type B packaging design carrying a novel fuel basket design with an incorporated flux trap. The basket can be loaded with 18 individual fuel canisters. The research collaboration investigated the U.S. certification potential of this concept. This part of the project included evaluations of criticality safety, radiological safety, thermal safety, structural integrity, and confinement under hypothetical accident scenarios of transport. The results of these evaluations demonstrated a promising potential for U.S. certification of this concept. Eventually, the described efforts led to the pursuance and issuance of a U.S. patent, thus, protecting the associated intellectual property (IP). Current short-term goals include making this IP available to private industry partners for licensing, directly supporting DOE’s objectives of accelerating commercialization of national laboratory-generated IP. If additional funding becomes available, long-term research goals could include exploring the feasibility of transporting other uranium chemical forms (e.g., UF4) with this concept, or refining operational procedures to load or unload the packagings.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Incorporating geological structure into sensitivity analysis of subsurface contaminant transport

Simulating subsurface contaminant transport at the kilometer-scale often entails modeling reactive flow and transport within and through complex geologic structures. These structures are typically meshed by hand and as a result geologic structure is usually represented by one or a few deterministically generated geological models for uncertainty studies of flow and transport in the subsurface. Uncertainty in geologic structure can have a significant impact on contaminant transport. In this study, the impact of geologic structure on contaminant tracer transport in a shale formation is investigated for a simplified generic deep geologic repository for permanent disposal of spent nuclear fuel. An open-source modeling framework is used to perform a sensitivity analysis study on transport of two tracers from a generic spent nuclear fuel repository with uncertain location of the interfaces between the stratum of the geologic structure. The automated workflow uses sampled realizations of the geological structural model in addition to uncertain flow parameters in a nested sensitivity analysis. Concentration of the tracers at observation points within, in line with, and downstream of the repository are used as the quantities of interest for determining model sensitivity to input parameters and geological realization. Finally, the results of the study indicate that the location of strata interfaces in the geological structure has a first-order impact on tracer transport in the example shale formation, and that this impact may be greater than that of the uncertain flow parameters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W