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At least 595 records · Page 33

Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures

Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.

mass spectrometry, FTICR, FTMS, ultrahigh mass res↗

Stress interference in multilayer additive friction stir deposition of AA6061 aluminum

Due to the multilayer deposition nature of metal additive manufacturing processes, each layer being printed experiences the state of thermokinetic and thermomechanical stress that in turn interfere with the state of thermokinetics and thermomechanical stress of subsequently deposited layers. Especially, this multilayer interference significantly affects the resultant properties of the component fabricated using solid-state additive friction stir deposition due to evolution of asymmetric state of planar stress. Due to the lack of comprehensive and suitable in situ diagnosis technique, the complex interference of inter- and multi-layer stresses during additive friction stir deposition was studied in an integrated approach of numerical simulation of fluidic state and experimental probing of stress influenced ultrasonic elastography. The uni-directional and bi-directional layer deposition configurations adopted during additive friction stir deposition result in the generation of constructive and destructive interference of the interlayer stress and hence, asymmetric and symmetric dynamic elasticity distribution respectively within the subsequent layers. With subsequent deposition of additional layers, the odd and even numbers of deposited layers generate asymmetric and nearly symmetric dynamic elasticity distributions.

Yang, Teng↗

Magnus method for electronic structure calculations at extreme conditions

We present the application of Magnus based methods to the solution of first order coupled ordinary differential equations in High Energy Density (HED) physics applications. Our focus is on the application to quantum mechanical methods, specifically on the solution of the radial Dirac equation for real and complex energies. HED applications require accurate solutions across a wide range of spatial and energy domains, including regimes where the solutions exhibit pronounced oscillatory behavior. Such cases pose significant computational challenges. We demonstrate that Magnus-based integrators can efficiently and accurately address these challenges. We discuss the implementation of the Magnus method for the solution of the radial Dirac equation, including practical considerations such as the evaluation of matrix exponentials, numerical integration, error estimation, and adaptive step size control. We also discuss the application of these methods to complex energy Green’s function techniques and the efficient approximation of integrals of the solutions relevant to HED electronic structure calculations. Here, we demonstrate the accuracy and robustness of the resulting method in applications to the free-particle case, for which analytic solutions are available for comparison, as well as the challenging case of gold at HED conditions.

general physics↗

Risk-averse optimal control of semilinear elliptic PDEs

In this paper, we consider the optimal control of semilinear elliptic PDEs with random inputs. These problems are often nonconvex, infinite-dimensional stochastic optimization problems for which we employ risk measures to quantify the implicit uncertainty in the objective function. In contrast to previous works in uncertainty quantification and stochastic optimization, we provide a rigorous mathematical analysis demonstrating higher solution regularity (in stochastic state space), continuity and differentiability of the control-to-state map, and existence, regularity and continuity properties of the control-to-adjoint map. Our proofs make use of existing techniques from PDE-constrained optimization as well as concepts from the theory of measurable multifunctions. We illustrate our theoretical results with two numerical examples motivated by the optimal doping of semiconductor devices.

97 MATHEMATICS AND COMPUTING↗

Anion diffusion in two-dimensional halide perovskites

Commercialization of halide perovskites in the semiconductor industry is hindered by their short-term stability. The instability of perovskites is closely interlinked with ionic diffusion. Historically, attempts to study diffusion in 2D perovskites mostly utilized electrical characterizations, but these characterizations pose a challenge in deconvoluting the impact of device architecture, interlayers, and ionic species. In this Perspective, we focus our attention on simple optical characterizations employed in the literature to investigate halide diffusion in 2D perovskites using lateral and vertical heterostructure platforms. We review the various synthesis techniques used for fabrication of halide perovskite heterostructures and discuss the qualitative and quantitative diffusion studies performed using these platforms. We discuss the numerical methods used to validate and supplement the experimental halide diffusion kinetics. Finally, we highlight the need to conduct further research on the impact of device operating conditions, lattice structure, and vacancy concentration on halide diffusion. Through this Perspective, we aim to emphasize the need of developing a comprehensive understanding of halide diffusion in perovskites for their successful deployment in optoelectronics.

36 MATERIALS SCIENCE↗

Measuring the thermal conductivity of hydrogels with a bidirectional 3w method

Hydrogels are soft, water-absorbing polymer materials with diverse applications in biomedicine and agriculture. Recently, hydrogels have been proposed to encapsulate water-soluble phase change materials which store energy in their latent heat of solidification. In these applications, the thermal conductivity of these materials affects their performance. Few methods exist for measuring the thermal conductivity of small quantities of hydrogels. Here, we describe an implementation of the bidirectional 3w technique to measure the thermal conductivity of hydrogels with particular attention to their moisture content. Our implementation of the technique can probe sample volumes as little as ~20 mL and yields the thermal conductivity without requiring fitting of additional thermal parameters. We numerically simulate 3w sensor designs with frequency-domain 3-D models to quantify and reduce errors introduced by the choice of substrate and insulation layer thickness. Frequencies in the ~1−20 Hz range yield less error for the materials considered here. We verify our setup with measurements on water and report values for polyacrylamide and poly(2-acrylamido-2-methylpropane sulfonic acid) (PAMPS) hydrogels. Our swollen hydrogels exhibited thermal conductivities nearly equivalent to water, 0.6 W m-1 K-1, and we estimate thermal conductivities of 0.43 and 0.42 W m-1 K-1 for neat polyacrylamide and PAMPS, respectively. Finally, we estimate an error of ±7%, consistent with other 3ω methods, with the largest error coming from the sensor calibration. We find our implementation of the bidirectional 3w method gives reasonable results and can be employed for prototyping soft materials relevant for thermal storage.

3-omega, thermal conductivity, hydrogel, moisture ↗

Cross slip of extended dislocations in face-centered cubic metals through phase-field modeling

Cross slip is a dislocation mechanism that significantly impacts the mechanical behavior of engineering alloys. Here, in this work, we advance a 3D phase-field dislocation dynamics (PFDD) mesoscale technique to simulate cross slip across a broad range of face-centered cubic (FCC) metals. The formulation incorporates elastic anisotropy, an FCC numerical grid, and a high-fidelity representation of the entire γ -surface from density functional theory for eight FCC metals and no adjustable parameters or rules. The relaxed core structures under zero stress for all metals are predicted to extend in plane. The analytical model for stacking fault width agrees well with the PFDD result under the assumption of elastic isotropy but overestimates it under elastic anisotropy, when the degree of anisotropy is large. The dynamic simulations are designed to elucidate the material parameters that influence the propensity for cross slip. Whether cross slip occurs under a non-Schmid stress or to bypass a hard obstacle, the critical stress to cross slip scales strongly with the anisotropic energy coefficient for a screw dislocation.

36 MATERIALS SCIENCE↗

Mesoscale to Microscale Coupling for Wind Energy Applications: Addressing the Challenges

The purpose of the US DOE's Mesoscale to Microscale Coupling (MMC) Project is to develop, verify, and validate physical models and modeling techniques that bridge the most important atmospheric scales that determine wind plant performance and reliability. The project seeks to create a new predictive numerical simulation capability that represents a range of dynamic atmospheric flow conditions impacting wind plant performance.

17 WIND ENERGY↗

Extracting and Interpreting Electrochemical Impedance Spectra (EIS) from Physics-Based Models of Lithium-Ion Batteries

This paper implements a highly efficient algorithm to extract electrochemical impedance spectra (EIS) from physics-based battery models (e.g., a P2D model). The mathematical approach is different from how EIS is practiced experimentally. Experimentally, the voltage (current) is harmonically perturbed over a wide range of frequencies and the amplitude and phase shift of the corresponding current (voltage) is measured. The experimental approach can be implemented in simulation software, but is computationally expensive. The approach here is to determine locally linear state-space models from the full physical model. The four Jacobian matrices that are the basis of the state-space models can be derived by numerical differentiation of the physical model. The EIS is then extracted from the state-space model using computationally efficient matrix-manipulation techniques. The algorithm can evaluate the full EIS at an instant in time during a transient, independent of whether the battery is in a stationary state. The approach is also able to separate the full-cell impedance to evaluate partial EIS, such as for a battery anode alone. Although such partial EIS is difficult to measure experimentally, the partial EIS provides valuable insights in interpreting the full-cell EIS.

25 ENERGY STORAGE↗

Parallel-In-Time Integration for Hyperbolic Problems (Final Report)

The work for the subcontract was situated in the area of parallel-in-time integration for advection-dominated and hyperbolic partial differential equations (PDEs). Parallel-in-time integration is an active area of research due to its ability to enable faster numerical simulations for applications throughout many areas of science. Over the past two decades, much progress has been made in this area; however, this progress has largely been limited to non-hyperbolic, diffusion-dominated PDEs. Given the ubiquity of numerical simulations of advection-dominated hyperbolic PDEs throughout the sciences, there is a strong need to develop efficient parallel-in-time techniques for hyperbolic problems, which was the main topic of this subcontract.

97 MATHEMATICS AND COMPUTING↗

Solving Coupled Cluster Equations by the Newton Krylov Method

We describe using the Newton Krylov method to solve the coupled cluster equation. The method uses a Krylov iterative method to compute the Newton correction to the approximate coupled cluster amplitude. The multiplication of the Jacobian with a vector, which is required in each step of a Krylov iterative method such as the Generalized Minimum Residual (GMRES) method, is carried out through a finite difference approximation, and requires an additional residual evaluation. The overall cost of the method is determined by the sum of the inner Krylov and outer Newton iterations. We discuss the termination criterion used for the inner iteration and show how to apply pre-conditioners to accelerate convergence. We will also examine the use of regularization technique to improve the stability of convergence and compare the method with the widely used direct inversion of iterative subspace (DIIS) methods through numerical examples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Long-term Dynamical Stability in the Outer Solar System. I. The Regular and Chaotic Evolution of the 34 Largest Trans-Neptunian Objects

We carried out an extensive analysis of the stability of the outer solar system, making use of the frequency analysis technique over short-term integrations of nearly 100,000 test particles, as well as a statistical analysis of 200 1 Gyr long numerical simulations, which consider the mutual perturbations of the giant planets and the 34 largest trans-Neptunian objects (we have called all 34 objects “dwarf planets,” DPs, even if probably only the largest of them are true DPs). From the frequency analysis, we produced statistical diffusion maps for a wide region of the a–e phase-space plane; we also present the average diffusion time for orbits as a function of perihelion. We later turned our attention to the 34 DPs, making an individualized analysis for each of them and producing a first approximation of their future stability. From the 200 distinct realizations of the orbital evolution of the 34 DPs, we classified the sample into three categories, including 17 stable, 11 unstable, and 6 resonant objects; we also found that, statistically, two objects from the sample will leave the trans-Neptunian region within the next gigayear, most likely being ejected from the solar system, but with a nonnegligible probability of going inside the orbit of Neptune, either to collide with a giant planet or even falling to the inner solar system, where our simulations are no longer able to resolve their continuous evolution.

79 ASTRONOMY AND ASTROPHYSICS↗

Two-moment Neutrino Flavor Transformation with Applications to the Fast Flavor Instability in Neutron Star Mergers

Abstract Multi-messenger astrophysics has produced a wealth of data with much more to come in the future. This enormous data set will reveal new insights into the physics of core-collapse supernovae, neutron star mergers, and many other objects where it is actually possible, if not probable, that new physics is in operation. To tease out different possibilities, we will need to analyze signals from photons, neutrinos, gravitational waves, and chemical elements. This task is made all the more difficult when it is necessary to evolve the neutrino component of the radiation field and associated quantum-mechanical property of flavor in order to model the astrophysical system of interest—a numerical challenge that has not been addressed to this day. In this work, we take a step in this direction by adopting the technique of angular-integrated moments with a truncated tower of dynamical equations and a closure, convolving the flavor-transformation with spatial transport to evolve the neutrino radiation quantum field. We show that moments capture the dynamical features of fast flavor instabilities in a variety of systems, although our technique is by no means a universal blueprint for solving fast flavor transformation. To evaluate the effectiveness of our moment results, we compare to a more precise particle-in-cell method. Based on our results, we propose areas for improvement and application to complementary techniques in the future.

Astronomy & Astrophysics↗

Bayesian Spatially Varying Multi-Regularization Image Deblurring

Many scientific experiments such as those found in astronomy, geology, microbiology, and X-ray radiography require the use of high-energy instruments to capture images. Since blur and noise are inevitably present in any imaging system, the images must be \deblurred" to extract the full information content. Mathematically, image deblurring is an ill-posed inverse problem that requires regularization. The regularization, in turn, has a large effect on the deblurred image: different regularization strengths, and types, lead to drastically different reconstructions. Moreover, many images contain a mixture of smooth and sharp features which suggests the use of multi-regularization, i.e., varying the type of regularization (e.g. Tikhonov or total variation) across the image. We address these issues by formulating the image deblurring problem within a hierarchical Bayesian framework in which we spatially adapt the strength of the regularization and also vary the regularization type across the image. In this way, the image itself, along with corresponding regularization strength at each pixel, are described jointly by a posterior distribution which we can sample by Markov chain Monte Carlo (MCMC) methods. We illustrate our techniques on simplified test problems and apply them to high-energy X-ray images taken at the Nevada National Security Site. Numerical tests show that our new method is robustly applicable and increases the quality of the image reconstruction when compared to other (Bayesian) methods.

97 MATHEMATICS AND COMPUTING↗

Recent Progress on Surface Water Quality Models Utilizing Machine Learning Techniques

Surface waterbodies are heavily exposed to pollutants caused by natural disasters and human activities. Empowering sensor technologies in water quality monitoring, sufficient measurements have become available to develop machine learning (ML) models. Numerous ML models have quickly been adopted to predict water quality indicators in various surface waterbodies. This paper reviews 78 recent articles from 2022 to October 2024, categorizing water quality models utilizing ML into three groups: Point-to-Point (P2P), which estimates the current target value based on other measurements at the same time point; Sequence-to-Point (S2P), which utilizes previous time series data to predict the target value at one time point ahead; and Sequence-to-Sequence (S2S), which uses previous time series data to forecast sequential target values in the future. The ML models used in each group are classified and compared according to water quality indicators, data availability, and model performance. Widely used strategies for improving performance, including feature engineering, hyperparameter tuning, and transfer learning, are recognized and described to enhance model effectiveness. The interpretability limitations of ML applications are discussed. This review provides a perspective on emerging ML for surface water quality models.

machine learning (ML)↗

Rare Event Sampling Improves Mercury Instability Statistics

Due to the chaotic nature of planetary dynamics, there is a non-zero probability that Mercury's orbit will become unstable in the future. Previous efforts have estimated the probability of this happening between 3 and 5 billion years in the future using a large number of direct numerical simulations with an N-body code, but were not able to obtain accurate estimates before 3 billion years in the future because Mercury instability events are too rare. In this paper we use a new rare-event sampling technique, Quantile Diffusion Monte Carlo (QDMC), to estimate that the probability of a Mercury instability event in the next 2 billion years is approximately 10 –4 in the REBOUND N-body code. We show that QDMC provides unbiased probability estimates at a computational cost of up to 100 times less than direct numerical simulation. QDMC is easy to implement and could be applied to many problems in planetary dynamics in which it is necessary to estimate the probability of a rare event.

79 ASTRONOMY AND ASTROPHYSICS↗

Universal energy-speed-accuracy trade-offs in driven nonequilibrium systems

The connection between measure theoretic optimal transport and dissipative nonequilibrium dynamics provides a language for quantifying nonequilibrium control costs, leading to a collection of thermodynamic speed limits, which rely on the assumption that the target probability distribution is perfectly realized. This is almost never the case in experiments or numerical simulations, so here we address the situation in which the external controller is imperfect. We obtain a lower bound for the dissipated work in generic nonequilibrium control problems that (1) is asymptotically tight and (2) matches the thermodynamic speed limit in the case of optimal driving. Along with analytically solvable examples, we refine this imperfect driving notion to systems in which the controlled degrees of freedom are slow relative to the nonequilibrium relaxation rate, and identify independent energy contributions from fast and slow degrees of freedom. Furthermore, we develop a strategy for optimizing minimally dissipative protocols based on optimal transport flow matching, a generative machine learning technique. Furthermore, this latter approach ensures the scalability of both the theoretical and computational framework we put forth. Crucially, we demonstrate that we can compute the terms in our bound numerically using efficient algorithms from the computational optimal transport literature and that the protocols we learn saturate the bound.

59 BASIC BIOLOGICAL SCIENCES↗

Reduced Dynamics of Full Counting Statistics

We present a theory of modified reduced dynamics in the presence of counting fields. Reduced dynamics techniques are useful for describing open quantum systems at long emergent timescales when the memory timescales are short. However, they can be difficult to formulate for observables spanning the system and its environment, such as those characterizing transport properties. A large variety of mixed system--environment observables, as well as their statistical properties, can be evaluated by considering counting fields. Given a numerical method able to simulate the field-modified dynamics over the memory timescale, we show that the long-lived full counting statistics can be efficiently obtained from the reduced dynamics. We demonstrate the utility of the technique by computing the long-time current in the nonequilibrium Anderson impurity model from short-time Monte Carlo simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗