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At least 397 records · Page 22

Physical effects at the cellular level under altered gravity conditions

Several modifications of differentiated functions of animal cells cultivated in vitro have been reported when cultures have been exposed to increased or decreased inertial acceleration fields by centrifugation, clinorotation, and orbital space flight. Variables modified by clinorotation conditions include inertial acceleration, convection, hydrostatic pressure, sedimentation, and shear stress, which also affect transport processes in the extracellular chemical environment. Autocrine, paracrine and endocrine substances, to which cells are responsive via specific receptors, are usually transported in vitro (and possibly in certain embryos) by convection and in vivo by a circulatory system or ciliary action. Increased inertial acceleration increases convective flow, while microgravity nearly abolishes it. In the latter case the extracellular transport of macromolecules is governed by diffusion. By making certain assumptions it is possible to calculate the Peclet number, the ratio of convective transport to diffusive transport. Some, but not all, responses of cells in vitro to modified inertial environments could be manifestations of modified extracellular convective flow.

Todd, Paul↗

Description of di-hadron saturation signals within a universal nuclear parton distribution function approach

Di-hadron and di-jet correlation measurements in proton-nucleus (𝑝+𝐴) and electron-nucleus collisions are widely motivated as sensitive probes of novel, nonlinear quantum chromodynamices saturation dynamics in hadrons, which are particularly accessible in the dense nuclear environment at low values of Bjorken-𝑥 (𝑥 A ). Current measurements at the BNL Relativistic Heavy Ion Collider (RHIC) and the CERN Large Hadron Collider (LHC) observe a significant suppression in the per-trigger yield at forward rapidities compared to that in proton-proton collisions, nominally consistent with the “mono-jet” production expected in a saturation scenario. However, the width of the azimuthal correlation remains unmodified, in contradiction to the qualitative expectations from this physics picture. I investigate whether the construction of these observables leaves them sensitive to effects from simple nuclear shadowing as captured by, for example, universal nuclear parton distribution function (nPDF) analyses. I find that modern nPDF sets, informed by recent precision measurements sensitive to the shadowing of low-𝑥 A gluon densities in LHC and other data, can describe all or the majority of the di-hadron/jet suppression effects in 𝑝+𝐴 data at both RHIC and the LHC, while giving a natural explanation for why the azimuthal correlation width is unmodified. Notably, this is achieved via a (𝑥 A ,𝑄 2 )-differential suppression of overall cross sections only, without requiring additional physics dynamics which alter the interevent correlations.

Jets & heavy flavor physics↗

Self-adaptive weights based on balanced residual decay rate for physics-informed neural networks and deep operator networks

Physics-informed deep learning has emerged as a promising alternative for solving partial differential equations. However, for complex problems, training these networks can still be challenging, often resulting in unsatisfactory accuracy and efficiency. In this work, we demonstrate that the failure of plain physics-informed neural networks arises from the significant discrepancy in the convergence rate of residuals at different training points, where the slowest convergence rate dominates the overall solution convergence. Based on these observations, we propose a pointwise adaptive weighting method that balances the residual decay rate across different training points. The performance of our proposed adaptive weighting method is compared with current state-of-the-art adaptive weighting methods on benchmark problems for both physics-informed neural networks and physics-informed deep operator networks. In conclusion, through extensive numerical results we demonstrate that our proposed approach of balanced residual decay rates offers several advantages, including bounded weights, high prediction accuracy, fast convergence rate, low training uncertainty, low computational cost, and ease of hyperparameter tuning.

Balanced convergence rate↗

Differentiating and Quantifying Gas-Phase Conformational Isomers Using Coulomb Explosion Imaging

Conformational isomerism plays a crucial role in defining the physical and chemical properties and biological activity of molecules ranging from simple organic compounds to complex biopolymers. However, it is often a significant challenge to differentiate and separate these isomers experimentally as they can easily interconvert due to their low rotational energy barrier. Here, we use the momentum correlation of fragment ions produced after inner-shell photoionization to distinguish conformational isomers of 1,2-dibromoethane (C 2 H 4 Br 2 ). We demonstrate that the three-body breakup channel, C 2 H 4 + + Br + + Br + , contains signatures of both sequential and concerted breakup, which are decoupled to distinguish the geometries of two conformational isomers and to quantify their relative abundance. The sensitivity of our method to quantify these yields is established by measuring the relative abundance change with sample temperature, which agrees well with calculations. Finally, our study paves the way for using Coulomb explosion imaging to track subtle molecular structural changes.

Photoionization↗

TPSAS-NF1676L-30451-DND

The fundamental laws of the physics of fluid flow in the continuum regime are embedded in a somewhat "simple" set of partial differential equations describing the transport of mass, momentum, energy, and/orentropy. These basic equations can be manipulated to construct other important physical quantities such as vorticity that help further elucidate flow physics. Additionally, these equations can be nondimensionalized to identify important nondimensional groups governing compressible, reacting fluid flows, most prominently Reynolds, Mach, Froude, Prandtl, Lewis, Schmidt, Damkohler, and Zeldovich numbers. In this lecture, we present these governing equations and discuss the significance of the different terms and nondimensional groups. Furthermore, since these equations cannot be solved directly on current supercomputers for turbulent flows at Reynolds numbers of engineering interest, a scale reduction by averaging or filtering is introduced, which leads to a "closure" problem. The closure is then provided by introducing some common models. The current introduction is by no means complete, but it and the references herein may serve as a good starting point for learning about the most common approaches to turbulent reacting flows.

Tomasz (Tom) G Drozda↗

Machine learning and algebraic approaches towards complete matter spectra in 4d F-theory

Motivated by engineering vector-like (Higgs) pairs in the spectrum of 4d F-theory compactifications, we combine machine learning and algebraic geometry techniques to analyze line bundle cohomologies on families of holomorphic curves. To quantify jumps of these cohomologies, we first generate 1.8 million pairs of line bundles and curves embedded in dP 3 , for which we compute the cohomologies. A white-box machine learning approach trained on this data provides intuition for jumps due to curve splittings, which we use to construct additional vector-like Higgs-pairs in an F-Theory toy model. We also find that, in order to explain quantitatively the full dataset, further tools from algebraic geometry, in particular Brill-Noether theory, are required. Using these ingredients, we introduce a diagrammatic way to express cohomology jumps across the parameter space of each family of matter curves, which reflects a stratification of the F-theory complex structure moduli space in terms of the vector-like spectrum. Furthermore, these insights provide an algorithmically efficient way to estimate the possible cohomology dimensions across the entire parameter space.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Generative Ensemble Regression: Learning Particle Dynamics from Observations of Ensembles with Physics-informed Deep Generative Models

Here, we propose a new method for inferring the governing stochastic ordinary differential equations (SODEs) by observing particle ensembles at discrete and sparse time instants, i.e., multiple “snapshots.” Particle coordinates at a single time instant, possibly noisy or truncated, are recorded in each snapshot but are unpaired across the snapshots. By training a physics-informed generative model that generates “fake” sample paths, we aim to fit the observed particle ensemble distributions with a curve in the probability measure space, which is induced from the inferred particle dynamics. We employ different metrics to quantify the differences between distributions, e.g., the sliced Wasserstein distances and the adversarial losses in generative adversarial networks. We refer to this method as generative “ensemble-regression” (GER), in analogy to the classic “point-regression,” where we infer the dynamics by performing regression in the Euclidean space. We illustrate the GER by learning the drift and diffusion terms of particle ensembles governed by SODEs with Brownian motions and Lévy processes up to 100 dimensions. We also discuss how to treat cases with noisy or truncated observations. Apart from systems consisting of independent particles, we also tackle nonlocal interacting particle systems with unknown interaction potential parameters by constructing a physics-informed loss function. Finally, we investigate scenarios of paired observations and discuss how to reduce the dimensionality in such cases by proving a convergence theorem that provides theoretical support.

97 MATHEMATICS AND COMPUTING↗

Improvements of Nuclear Data Evaluations for Lead Isotopes in Support of Next Generation Lead-Cooled Fast Systems

The neutron evaluation of the isotopes that comprise natural lead were undertaken as a part of DOE-NEUP Project #19-16739. The goal of the project was to update the neutron cross sections to account for new differential measurements and incorporate the most up-to-date physics. Shortcomings in the lead cross sections was made known by several independent reports. The work performed here repeated the simulation of all the “benchmark” validation systems and concluded that the major issue is the scattering cross sections in the major lead isotopes above 100 keV. Re-evaluation of 206,207,208 Pb included both the resolved resonance region and fast region evaluations of the cross sections. Combined these regions cover energies from thermal to 20 MeV. The most drastic improvement is the resolved resonance region evaluation of 208 Pb which is now extended from 1.0 to 1.5 MeV. Parameterization of these resonances in the R-matrix provides a superior reconstruction of not only the experimental cross section but also the scattering distributions via the Blatt-Biedenharn formalism. Fast region evaluations of the three major isotopes were done to include new inelastic experimental data from the neutron Time-of-Flight facility at CERN. The culmination of all the changes to the cross section is a drastic improvement in the scattering kernel as shown in Rensselaer Polytechnic Institute (RPI) Quasi-Differential scattering measurements and improved prediction of keff for fast integral experiments. Alongside the new cross sections, new nuclear data covariance (uncertainties) have been computed and are included in the evaluation. Little is changed in the magnitude of the uncertainties but the correlations within the covariance display non-trivial changes. The new evaluations of 206,207,208 Pb have been submitted to the National Nuclear Data Center to be included in the ENDF/B-VIII.1 library. While the cross sections have been updated extensively, knowledge and modeling of the cross sections between 1.0 and 3.0 MeV for the isotopes remain a challenge. Most notably is the double differential elastic cross section for 208 Pb and 206 Pb. New quasi-differential measurements for pure samples of these two nuclei would go a long way in reducing compensating errors in the evaluations. Qualitatively, the project has produced a prosperous collaboration between the nuclear data group at RPI with staff scientists at Brookhaven National Laboratory, Naval Nuclear Laboratory, Oak Ridge National Laboratory, Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratories. Quantitatively this is reflected in seven conference presentations, at least one journal submission, and one doctoral thesis.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Geometry optimization speedup through a geodesic approach to internal coordinates

We present a new geodesic-based method for geometry optimization in a basis set of redundant internal coordinates. Overall, our method updates the molecular geometry by following the geodesic generated by a displacement vector on the internal coordinate manifold, which dramatically reduces the number of steps required to converge to a minimum. Our method can be implemented in any existing optimization code, requiring only implementation of derivatives of the Wilson B-matrix and the ability to numerically solve an ordinary differential equation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lunar and Planetary Science Conference, 11th, Houston, TX, March 17-21, 1980, Proceedings. Volume 1 - Igneous processes and remote sensing

Topics discussed include basaltic studies, planetary differentiation (e.g., lunar highland rocks), and remote sensing studies of chemical composition, mineralogic composition, and physical surface properties. Particular attention is given to the petrology and chemistry of basaltic fragments from the Apollo 11 soil; a model of early lunar differentiation; rocks of the early lunar crust; refractory and moderately volatile element abundances in the earth, moon, and meteorites; the effects of overlapping optical absorption bands of pyroxene and glass on the reflectance spectra of lunar soils; and the characterization of Martian surface materials from earth-based radar.

Merrill, R. B.↗

Learning effective stochastic differential equations from microscopic simulations: Linking stochastic numerics to deep learning

We identify effective stochastic differential equations (SDEs) for coarse observables of fine-grained particle- or agent-based simulations; these SDEs then provide useful coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDEs through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler–Maruyama and Milstein); our approximations can thus benefit from backward error analysis of these underlying numerical schemes. They also lend themselves naturally to “physics-informed” gray-box identification when approximate coarse models, such as mean field equations, are available. Existing numerical integration schemes for Langevin-type equations and for stochastic partial differential equations can also be used for training; we demonstrate this on a stochastically forced oscillator and the stochastic wave equation. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

97 MATHEMATICS AND COMPUTING↗

Stability-preserving Lossy Compression for Large-scale Partial Differential Equations

Checkpoint/Restart (C/R) strategies are vital for fault tolerance in PDE-based scientific simulations, yet traditional checkpointing incurs significant I/O overhead. Lossy compression offers a scalable solution by reducing checkpoint data size, but conventional methods often lack control over physical invariants (e.g., energy), leading to instability such as oscillations or divergence in Partial Differential Equations (PDE) systems. This paper introduces a stability-preserving compression approach tailored for PDE simulations by explicitly controlling kinetic and potential energy perturbations to ensure stable restarts. Extensive experiments conducted across diverse PDE configurations demonstrate that our method maintains numerical stability with minimal error magnification—even across multiple checkpoint-restart cycles—outperforming state-of-the-art lossy compressors. Parallel evaluations on the Frontier supercomputer show up to 8.4× improvement in checkpoint write performance and 6.3× in read performance, while maintaining relative L2 errors ∼ 2e-6 throughout continued simulation. These results provide practical guidance for balancing compression accuracy, stability, and computational efficiency in large-scale PDE applications.

Gong, Qian [ORNL] (ORCID:0000000235704142)↗

Cosmology meets cohomology

The cosmological polytope and bootstrap programs have revealed interesting connections between positive geometries, modern on-shell methods and bootstrap principles studied in the amplitudes community with the wavefunction of the Universe in toy models of FRW cosmologies. To compute these FRW correlators, one often faces integrals that are too difficult to evaluate by direct integration. Borrowing from the Feynman integral community, the method of (canonical) differential equations provides an efficient alternative for evaluating these integrals. Moreover, we further develop our geometric understanding of these integrals by describing the associated relative twisted cohomology. Leveraging recent progress in our understanding of relative twisted cohomology in the Feynman integral community, we give an algorithm to predict the basis size and simplify the computation of the differential equations satisfied by FRW correlators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A neural master equation framework for multiscale modeling of molecular processes: application to atomic-scale plasma processes

Plasma-surface interactions (PSI) play a crucial role in microelectronics fabrication; however, their multiscale nature and array of complex, often unknown interactions make computational modeling of PSIs extremely difficult. To this end, we propose a general neural master equation (NME) framework that uses master equations to describe the dynamics of a molecular process, wherein neural networks learned from atomistic simulations represent unknown transitions between different system states. By leveraging the physics-based structure of master equations and data-driven state transitions, the NME framework promotes generalizability and physics interpretability, and can bridge disparate length and time scales. The framework is demonstrated for multiscale modeling of Si atomic layer etching and reactive ion etching, where the learned NME-based surface kinetic models exhibit good predictive and extrapolative capabilities for predicting experimentally relevant observables as a function of process parameters. The NME-based surface kinetic models obey physical constraints, which are violated in models based on neural ordinary differential equations. The proposed NME framework for multiscale modeling of molecular processes can pave the way for the discovery of new chemistries and materials in atomic-scale plasma processes.

Chemical engineering↗

Learning Physically Interpretable Atmospheric Models From Data With WSINDy

The multiscale and turbulent nature of Earth's atmosphere has historically rendered accurate weather modeling a hard problem. Recently, there has been an explosion of interest surrounding data-driven approaches to weather modeling, which in many cases show improved forecasting accuracy and computational efficiency when compared to traditional methods. However, many of the current data-driven approaches employ highly parameterized neural networks, often resulting in uninterpretable models and limited gains in scientific understanding. In this work, we address the interpretability problem by explicitly discovering partial differential equations governing atmospheric phenomena, identifying symbolic mathematical models with direct physical interpretations. The purpose of this paper is to demonstrate that, in particular, the weak-form sparse identification of nonlinear dynamics (WSINDy) algorithm can learn effective atmospheric models from both simulated and assimilated data. Our approach adapts the standard WSINDy algorithm to work with high-dimensional fluid data of arbitrary spatial dimension.

58 GEOSCIENCES↗

Tetranuclear Polypyridylruthenium(II) Complexes as Selective Nucleic Acid Stains for Flow Cytometric Analysis of Monocytic and Epithelial Lung Carcinoma Large Extracellular Vesicles

Selective staining of extracellular vesicles (EVs) is a major challenge for diagnostic and therapeutic applications. Herein, the EV labeling properties of a new class of tetranuclear polypyridylruthenium(II) complexes, Rubb7-TNL and Rubb7-TL, as phosphorescent stains are described. These new stains have many advantages over standard stains to detect and characterize EVs, including: high specificity for EV staining versus cell staining; high phosphorescence yields; photostability; and a lack of leaching from EVs until incorporation with target cells. As an example of their utility, large EVs released from control (basal) or lipopolysaccharide (LPS)-stimulated THP-1 monocytic leukemia cells were studied as a model of immune system EVs released during bacterial infection. Key findings from EV staining combined with flow cytometry were as follows: (i) LPS-stimulated THP-1 cells generated significantly larger and more numerous large EVs, as compared with those from unstimulated cells; (ii) EVs retained native EV physical properties after staining; and (iii) the new stains selectively differentiated intact large EVs from artificial liposomes, which are models of cell membrane fragments or other lipid-containing debris, as well as distinguished two distinct subpopulations of monocytic EVs within the same experiment, as a result of biochemical differences between unstimulated and LPS-stimulated monocytes. Comparatively, the staining patterns of A549 epithelial lung carcinoma-derived EVs closely resembled those of THP-1 cell line-derived EVs, which highlighted similarities in their selective staining despite their distinct cellular origins. This is consistent with the hypothesis that these new phosphorescent stains target RNA within the EVs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

What do physics-informed DeepONets learn? Understanding and improving training for scientific computing applications

Physics-informed deep operator networks (DeepONets) have emerged as a promising approach toward numerically approximating the solution of partial differential equations (PDEs). In this work, we aim to develop further understanding of what is being learned by physics-informed DeepONets by assessing the universality of the extracted basis functions and demonstrating their potential toward model reduction with spectral methods. Results provide clarity about measuring the performance of a physics-informed DeepONet through the decays of singular values and expansion coefficients. In addition, we propose a transfer learning approach for improving training for physics-informed DeepONets between parameters of the same PDE as well as across different, but related, PDEs where these models struggle to train well. This approach results in significant error reduction and learned basis functions that are more effective in representing the solution of a PDE.

Deep operator networks↗