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At least 1,423 records · Page 79

Molecular mechanism of biased signaling at the kappa opioid receptor

The κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.

59 BASIC BIOLOGICAL SCIENCES↗

Complexity-calibrated benchmarks for machine learning reveal when prediction algorithms succeed and mislead

Abstract Recurrent neural networks are used to forecast time series in finance, climate, language, and from many other domains. Reservoir computers are a particularly easily trainable form of recurrent neural network. Recently, a “next-generation” reservoir computer was introduced in which the memory trace involves only a finite number of previous symbols. We explore the inherent limitations of finite-past memory traces in this intriguing proposal. A lower bound from Fano’s inequality shows that, on highly non-Markovian processes generated by large probabilistic state machines, next-generation reservoir computers with reasonably long memory traces have an error probability that is at least $$\sim 60\%$$ ∼ 60 % higher than the minimal attainable error probability in predicting the next observation. More generally, it appears that popular recurrent neural networks fall far short of optimally predicting such complex processes. These results highlight the need for a new generation of optimized recurrent neural network architectures. Alongside this finding, we present concentration-of-measure results for randomly-generated but complex processes. One conclusion is that large probabilistic state machines—specifically, large $$\epsilon$$ ϵ -machines—are key to generating challenging and structurally-unbiased stimuli for ground-truthing recurrent neural network architectures.

97 MATHEMATICS AND COMPUTING↗

Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold

Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗

Particle-in-cell modeling of electron beam generated plasma

Plasmas generated using energetic electron beams are well known for their low electron temperature (T e ) and plasma potential, which makes them attractive for atomic-precision plasma processing applications such as atomic layer etch and deposition. A 2-dimensional particle-in-cell model for an electron beam-generated plasma in argon confined by a constant applied magnetic field is described here in this article. Plasma production primarily occurs in the path of the beam electrons in the center of the chamber. The resulting plasma spreads out in the chamber through non-ambipolar diffusion with a short-circuiting effect allowing unequal electron and ion fluxes to different regions of the bounding conductive chamber walls. The cross-field transport of the electrons (and thus the steady-state characteristics of the plasma) are strongly impacted by the magnetic field. T e is anisotropic in the electron beam region, but low and isotropic away from the plasma production zone. The plasma density increases and the plasma becomes more confined near the region of production when the magnetic field strengthens. The magnetic field reduces both electron physical and energy transport perpendicular to the magnetic field. T e is uniform along the magnetic field lines and slowly decreases perpendicular to it. Electrons are less energetic in the sheath regions where the sheath electric field repels and confines the low-energy electrons from the bulk plasma. Even though electron and ion densities are similar in the bulk plasma due to quasi-neutrality, electron and ion fluxes on the grounded chamber walls are unequal at most locations. Electron confinement by the magnetic field weakens with increasing pressure, and the plasma spread out farther from the electron beam region.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Learning to classify quantum phases of matter with a few measurements

We study the identification of quantum phases of matter, at zero temperature, when only part of the phase diagram is known in advance. Following a supervised learning approach, we show how to use our previous knowledge to construct an observable capable of classifying the phase even in the unknown region. By using a combination of classical and quantum techniques, such as tensor networks, kernel methods, generalization bounds, quantum algorithms, and shadow estimators, we show that, in some cases, the certification of new ground states can be obtained with a polynomial number of measurements. An important application of our findings is the classification of the phases of matter obtained in quantum simulators, e.g. cold atom experiments, capable of efficiently preparing ground states of complex many-particle systems and applying simple measurements, e.g. single qubit measurements, but unable to perform a universal set of gates.

quantum machine learning↗

Mesogenesis through the ephemeral dark decay of Beauty

Mesogenesis provides a path for generating the baryon asymmetry of the Universe, using only the CP violation furnished by the Standard Model in the decay of B mesons. While this is an intriguing possibility, it is largely constrained by the data on B meson branching fractions into baryons and missing energy carried into the dark sector. We point out that it is possible to make this branching fraction dominant only in the early Universe, through an ultralight scalar coupled to the dark sector and the Standard Model leptons. A scenario is examined where the thermal density of muons in the early Universe temporarily lowers the mass of a dark fermion, allowing for efficient B meson decays. This `dark’ decay channel is shut off later when the muon number density falls, making the scenario compatible with flavor data. Our model can be consistent with the LHC constraints on color-charged heavy bosons required to implement Mesogenesis; such states may be discovered in the future runs as their masses cannot be far above the current bounds. We also outline other possible signals, which can arise in future displaced vertex searches, long range force searches, and observations of neutron star binary mergers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Past-completeness of inflationary spacetimes

Here, we discuss the question of whether or not inflationary spacetimes can be geodesically complete in the infinite past. Geodesic completeness is a necessary condition for averting an initial singularity during eternal inflation. It is frequently argued that cosmological models which are expanding sufficiently fast (having average Hubble expansion rate H avg > 0) must be incomplete in null and timelike past directions. This well-known conjecture relies on specific bounds on the integral of the Hubble parameter over a past- directed timelike or null geodesic. As stated, we show this claim is an open issue. We show that the calculation of H avg yields a continuum of results for a given spacetime predicated upon the underlying topological assumptions. We present an improved definition for H avg and introduce an uncountably infinite cohort of cosmological solutions which are geodesically complete despite having H avg > 0. We discuss a standardized definition for inflationary spacetimes as well as quantum (semiclassical) cosmological concerns over physically reasonable scale factors.

79 ASTRONOMY AND ASTROPHYSICS↗

Photovoltaic Inverter Failure Mechanism Estimation Using Unsupervised Machine Learning and Reliability Assessment

This article introduces a data-driven approach to assessing failure mechanisms and reliability degradation in outdoor photovoltaic (PV) string inverters. The manufacturer's stated PV inverter lifetime can vary due to the impact of operating site conditions. To address limitations in degradation estimation through accelerated testing, condition monitoring, or degradation modeling, we propose a machine learning (ML) oriented approach. Utilizing data from a 1.4 MW PV power plant operational since 2016, with 46 string PV inverters tied to the grid, we employ the unsupervised one-class support vector machine ML technique to analyze inverter and sensor data, capable of classifying humidity cycling and temperature fluctuations as dominant failure mechanisms. Utilizing the anomaly alert relationship and alert details specific to the inverter, the level of PV inverter output is considered as its availability or available reliability. Subsequently, a continuous Markov model is applied to six-month alert data, revealing an average stated reliability of 20% after 20 years of continuous operation. These results support recommendations for time-bound preventive measures to enhance PV inverter reliability under diverse outdoor conditions. Furthermore, the approach provides a nondestructive, top–down, and generalized method for analyzing any commercial PV inverter exposed to outdoor conditions, contingent on the availability of relevant data.

14 SOLAR ENERGY↗

A membrane-based approach to medical isotope purification (Final Report)

This is the final technical report from the grant "A membrane-based approach to medical isotope purification" which was awarded by the Isotope Research and Development Program through the early career research program to Christine Duval at Case Western Reserve University. The project developed adsoprtive membranes with covalently bound diglycolamide-derived ligands for the purification of Ac-225 and benchmarked them against the current state of the art adsorbent materials.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Iodide uptake by forest soils is principally related to the activity of extracellular oxidases

129 I is a nuclear fission decay product of concern because of its long half-life (16 Ma) and propensity to bioaccumulate. Microorganisms impact iodine mobility in soil systems by promoting iodination (covalent binding) of soil organic matter through processes that are not fully understood. Here, we examined iodide uptake by soils collected at two depths (0–10 and 10–20 cm) from 5 deciduous and coniferous forests in Japan and the United States. Autoclaved soils, and soils amended with an enzyme inhibitor (sodium azide) or an antibacterial agent (bronopol), bound significantly less 125 I tracer (93%, 81%, 61% decrease, respectively) than the untreated control soils, confirming a microbial role in soil iodide uptake. Correlation analyses identified the strongest significant correlation between 125 I uptake and three explanatory variables, actinobacteria soil biomass ( p = 6.04E-04, 1.35E-02 for Kendall-Tau and regression analysis, respectively), soil nitrogen content ( p = 4.86E-04, 4.24E-03), and soil oxidase enzyme activity at pH 7.0 using the substrate L-DOPA ( p = 2.83E-03, 4.33E-04) and at pH 5.5 using the ABTS ( p = 5.09E-03, 3.14E-03). Together, the results suggest that extracellular oxidases, primarily of bacterial origin, are the primary catalyst for soil iodination in aerobic, surface soils of deciduous and coniferous forests, and that soil N content may be indicative of the availability of binding sites for reactive iodine species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The energy separation between the classical and nonclassical isomers of protonated acetylene - An extensive study in one- and n-particle space saturation

The energy separation between the classical and nonclassical forms of protonated acetylene has been reinvestigated in light of the recent experimentally deduced lower bound to this value of 6.0 kcal/mol. The objective of the present study is to use state-of-the-art ab initio quantum mechanical methods to establish this energy difference to within chemical accuracy (i.e., about 1 kcal/mol). The one-particle basis sets include up to g-type functions and the electron correlation methods include single and double excitation coupled-cluster (CCSD), the CCSD(T) extension, multireference configuration interaction, and the averaged coupled-pair functional methods. A correction for zero-point vibrational energies has also been included, yielding a best estimate for the energy difference between the classical and nonclassical forms of 3.7 + or - 1.3 kcal/mol.

Lindh, Roland↗

Analytical Algorithms to Quantify the Uncertainty in Remaining Useful Life Prediction

This paper investigates the use of analytical algorithms to quantify the uncertainty in the remaining useful life (RUL) estimate of components used in aerospace applications. The prediction of RUL is affected by several sources of uncertainty and it is important to systematically quantify their combined effect by computing the uncertainty in the RUL prediction in order to aid risk assessment, risk mitigation, and decisionmaking. While sampling-based algorithms have been conventionally used for quantifying the uncertainty in RUL, analytical algorithms are computationally cheaper and sometimes, are better suited for online decision-making. While exact analytical algorithms are available only for certain special cases (for e.g., linear models with Gaussian variables), effective approximations can be made using the the first-order second moment method (FOSM), the first-order reliability method (FORM), and the inverse first-order reliability method (Inverse FORM). These methods can be used not only to calculate the entire probability distribution of RUL but also to obtain probability bounds on RUL. This paper explains these three methods in detail and illustrates them using the state-space model of a lithium-ion battery.

Sankararaman, Shankar↗

Analytical Methodology Used To Assess/Refine Observatory Thermal Vacuum Test Conditions For the Landsat 8 Data Continuity Mission

Thermal and Fluids Analysis Workshop Silver Spring, MD NCTS 21070-15 The Landsat 8 Data Continuity Mission, which is part of the United States Geologic Survey (USGS), launched February 11, 2013. A Landsat environmental test requirement mandated that test conditions bound worst-case flight thermal environments. This paper describes a rigorous analytical methodology applied to assess refine proposed thermal vacuum test conditions and the issues encountered attempting to satisfy this requirement.

0000↗

Robust adaptive regulation without persistent excitation

A globally convergent adaptive regulator for minimum or nonminimum phase systems subject to bounded distrubances and unmodeled dynamics is presented. The control strategy is designed for a particular input-output representation obtained from the state space representation of the system. The leading coefficient of the new representation is the product of the observability and controllability matrices of the system. The controller scheme uses a Least Squares identification algorithm with a dead zone. The dead zone is chosen to obtain convergence properties on the estimates and on the covariance matrix as well. This allows the definition of modified estimates which secure well-conditioned matrices in the adaptive control law. Explicit bounds on the plant output are given.

Lozano-Leal, Rogelio↗

Robust adaptive regulation without persistent excitation

A globally convergent adaptive regulator for minimum- or nonminimum-phase systems subject to bounded disturbances and unmodeled dynamics is presented. The control strategy is designed for a particular input-output representation obtained from the state space representation of the system. The leading coefficient of the representation is the product of the observability and controllability matrices of the system. The controller scheme uses a Least-Squares identification algorithm a with dead zone. The dead zone is chosen to obtain convergence properties on the estimates and on the covariance matrix as well. This allows the definition of modified estimates which secure well-conditioned matrices in the adaptive control law. Explicit bounds on the plant output are given.

Lozano-Leal, Rogelio↗

A General Framework for Error-controlled Unstructured Scientific Data Compression

Data compression plays a key role in reducing storage and I/O costs. Traditional lossy methods primarily target data on rectilinear grids and cannot leverage the spatial coherence in unstructured mesh data, leading to suboptimal compression ratios. We present a multi-component, error-bounded compression framework designed to enhance the compression of floating-point unstructured mesh data, which is common in scientific applications. Our approach involves interpolating mesh data onto a rectilinear grid and then separately compressing the grid interpolation and the interpolation residuals. This method is general, independent of mesh types and typologies, and can be seamlessly integrated with existing lossy compressors for improved performance. We evaluated our framework across twelve variables from two synthetic datasets and two real-world simulation datasets. The results indicate that the multi-component framework consistently outperforms state-of-the-art lossy compressors on unstructured data, achieving, on average, a 2.3 − 3.5× improvement in compression ratios, with error bounds ranging from 1 × 10 the −6 to 1×10−2. We further investigate impact of hyperparameters, such as grid spacing and error allocation, to deliver optimal compression ratios in diverse datasets.

Gong, Qian↗

Converging towards atomic and nuclear pressures (Final Report)

his report details the development of transformational tools and techniques, allowing the accurate characterization of matter at the most extreme conditions yet studied in the high energy density (HED) domain. Before this work, most experiments quantitatively mapping the nature of matter in the HED realm were performed using planar geometry, which allows for the isolation and measurement of variables in a single thermodynamic state. Such measurements include equation of state variables, optical conductivity, heat transport and more. However, due to a variety of plasma processes, such experiments are limited to below ~10 TPa (100 Mbar) pressures. To achieve higher pressures, convergent experiments are needed. Historically, convergent experiments have not been used for benchmark data because they are integral measurements. That is each part of a convergent target undergoes a time dependent wide range of states, making it difficult to accurately isolate any particular quantity for a given thermodynamic state. This effort developed innovative convergent HED platforms and techniques enabling the exploration of matter from atomic to nuclear scale pressures. This effort also performed pioneering experiments that yielded the first rigorous benchmark data at these extreme conditions. This funding award began with the overarching goal to understand the behavior of matter at extreme (atomic-to-nuclear scale) pressures. The motivation for these goals lie in the fact that every time scientists explore matter beyond the threshold of an atomic unit, there is a fundamental shift in science. The atomic unit for energy, mass, charge, length, and time have each been explored, and each time such a threshold was crossed, a new sequence of discoveries was made resulting in significant awards such as the Nobel Prize. The only unexplored atomic unit is pressure, and this effort set the course for exploring matter at and beyond such pressures. That most of the recently discovered extrasolar planets and stars, as well as matter in the late implosion stages of inertial fusion targets, have deep internal pressures at and beyond atomic pressures amplifies the importance of this effort. Much of the initial work in developing techniques to create these atomic-to-nuclear pressures already existed within the HED community, predominantly at large scale laser facilities such as the National Ignition Facility (NIF) and the Omega60 laser the University of Rochester and although these experiments were routinely performed the ability to extract information about the underlying physical states and processes remained elusive due to the complexity of the experiments, extreme scales in both time and space, and the integrated nature of all the measurements. This work built a rigorous framework so such measurements can routinely be made. This was done in part through the introduction of Bayesian inference techniques into the field of HED science. These techniques allow for the self-consistent extraction of the relevant variables and their explicit and implicit correlations, so as to make use of integrated experimental data to constrain physical models and provide accurate uncertainty bounds for the data. The techniques developed here are fully transparent and proved immediately useful providing quantitative rigorous benchmarks for physical states and processes at some of the most extreme conditions yet explored on Earth. This funding is directly or partly responsible for 7 publications in major peer-reviewed scientific journals, a doctoral thesis, 3 invited talks at major conferences, and the training of a post-doc, 2 graduate students, and 1 undergraduate student. Beyond the effort supported by this award launched the introduction of Bayesian inference into the HED physics community and helped push the usage if modern data-science techniques within the physics community at large.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Tetraquark Production by Intrinsic Charm

A number of new four-quark states containing from one to four c or ̅c quarks have been observed recently. Many of these new states have been discovered at the LHC. The production of these states via intrinsic charm in the proton is investigated. The tetraquark masses obtained in this approach, agree well with the measured masses. These calculations can provide some insight into the nature of the tetraquark candidates, whether as a bound meson pair or as a looser configuration of four individual partons which can influence their interactions in nuclear medium, such as in heavy-ion collisions. The kinematic distributions of these states as a function of y and pT are also studied. The possible cross sections for these states are also considered.

Vogt, Ramona [Lawrence Livermore National Laborato↗