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At least 109 records · Page 6

An arbitrarily high-order three-dimensional Cartesian-grid method for reconstructing interfaces from volume fraction fields

Here Tthis work describes a newly developed, arbitrarily high-order Cartesian-grid method for reconstructing material interfaces from a volume fraction field. The method begins by identifying all of the grid cells in the volume fraction field that are intersected by the interface and need to be approximated by the reconstruction scheme. Finite-differences are used to calculate the gradient of the volume fraction field and provide an estimate of the surface normal in all of the interfacial grid cells. Groups of connected grid cells are then identified which all have the same dominant component of the normal vector. This grouping by orientation determines the proper dependent variable to use in the surface reconstruction (e.g. for a 2D curve, this step determines if the surface will be approximated by a function of x or y). A cumulative integral over the surface is constructed and fit using b-splines for two-dimensional problems or tensor-product b-splines for three-dimensional problems. This construction allows for the interface to be recovered through application of the second fundamental theorem of calculus. Fitting the cumulative integral with $\mathscr{N}$ th-order b-splines (or tensor-product b-splines) yields an ($\mathscr{N}$-1) th-order convergence rate of the interface shape. Differentiation of the b-spline interface function(s) allows for the high-order approximation of the normal vector and curvature to be obtained directly anywhere along b-spline. Together, the proposed reconstruction technique can achieve arbitrarily high mesh convergence rates. Validation tests are presented with mesh convergence rates ranging from fourth- to tenth-order.

97 MATHEMATICS AND COMPUTING↗

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.

59 BASIC BIOLOGICAL SCIENCES↗

Application of Recursive Estimation to Heat Tracing for Groundwater/Surface‐Water Exchange

Abstract We present and demonstrate a recursive‐estimation framework to infer groundwater/surface‐water exchange based on temperature time series collected at different vertical depths below the sediment/water interface. We formulate the heat‐transport problem as a state‐space model (SSM), in which the spatial derivatives in the convection/conduction equation are approximated using finite differences. The SSM is calibrated to estimate time‐varying specific discharge using the Extended Kalman Filter (EKF) and Extended Rauch‐Tung‐Striebel Smoother (ERTSS). Whereas the EKF is suited to real‐time (“online”) applications and uses only the past and current measurements for estimation (filtering), the ERTSS is intended for near‐real time or batch‐processing (“offline”) applications and uses a window of data for batch estimation (smoothing). The two algorithms are demonstrated with synthetic and field‐experimental data and are shown to be efficient and rapid for the estimation of time‐varying flux over seasonal periods; further, the recursive approaches are effective in the presence of rapidly changing flux and (or) nonperiodic thermal boundary conditions, both of which are problematic for existing approaches to heat tracing of time‐varying groundwater/surface‐water exchange.

54 ENVIRONMENTAL SCIENCES↗

Capping layer influence and isotropic in-plane upper critical field of the superconductivity at the FeSe / SrTiO 3 interface

Understanding the superconductivity at the interface of FeSe/SrTiO 3 is a problem of great contemporary interest due to the significant increase in critical temperature (T c ) compared to that of bulk FeSe, as well as the possibility of an unconventional pairing mechanism and topological superconductivity. We report a study of the influence of a capping layer on superconductivity in thin films of FeSe grown on SrTiO 3 using molecular beam epitaxy. We used in vacuo four-probe electrical resistance measurements and ex situ magnetotransport measurements to examine the effect of three capping layers that provide distinct charge transfer into FeSe: insulating FeTe, nonmetallic Te, and metallic Zr. Our results show that FeTe provides an optimal cap that barely influences the inherent T c found in pristine FeSe/SrTiO 3 , while the transfer of holes from a nonmetallic Te cap completely suppresses superconductivity and leads to insulating behavior. Finally, we used ex situ magnetoresistance measurements in FeTe capped FeSe films to extract the angular dependence of the in-plane upper critical magnetic field. Our observations reveal an almost isotropic in-plane upper critical field, providing insight into the symmetry and pairing mechanism of high-temperature superconductivity in FeSe.

36 MATERIALS SCIENCE↗

An Efficient Checkpointing System for Large Machine Learning Model Training

As machine learning models increase in size and complexity rapidly, the cost of checkpointing in ML training became a bottleneck in storage and performance (time). For example, the latest GPT-4 model has massive parameters at the scale of 1.76 trillion. It is highly time and storage consuming to frequently writes the model to checkpoints with more than 1 trillion floating point values to storage. This work aims to understand and attempt to mitigate this problem. First, we characterize the checkpointing interface in a collection of representative large machine learning/language models with respect to storage consumption and performance overhead. Second, we propose the two optimizations: i) A periodic cleaning strategy that periodically cleans up outdated checkpoints to reduce the storage burden; ii) A data staging optimization that coordinates checkpoints between local and shared file systems for performance improvement.

machine learning, artificial intelligence↗

Data-Driven Modeling and Control of Systems with Plasma-Surface Interactions (Final Technical Report)

This final technical report summarizes the activities and accomplishments in the period from February 2023 thru January 2026. The objective of the proposed research is to investigate the physical mechanisms and processes underlying the formation of structures and patterns in systems with plasma-surface interactions. In the past decades, there have been extensive studies on the interaction of glow discharges, dielectric barrier discharges, and arc discharges with confining or intervening surfaces. The advancement of the understanding of these phenomena is not only of fundamental scientific interest and relevance to the knowledge of the plasma state, but also with profound implications in various technological applications. The research will integrate theoretical, computational, and experimental work within an innovative framework of data assimilation, i.e., optimally combining model predictions with measurements. The scientific merit of this research has three aspects. Firstly, it extends the studies of plasma-surface interactions to systems with insulator surfaces and multi-layer systems, while existing studies are predominantly on electrode surfaces. Secondly, it expects to develop a novel data-driven modeling approach based on data assimilation to enhance the predictive and control capabilities, which could make transformative contributions to basic plasma research. Thirdly, it will shed new light on outstanding problems related to formation of patterns interfacing plasmas. This project also aims to launch an education and outreach initiative at Texas A&M University-Kingsville, a non-R1, minority-serving institution in South Texas. The initiative is structured as a four-tier pyramid. Tier one will be a webinar series for culture and capacity building to inform broader audience in the region about the research fields of plasma science and engineering. Tier two will be the creation and offering of an upper-level undergraduate course on introductory plasma physics, which will help with the recruitment for the upper tiers. On tier three, we will engage and mentor senior design students to conduct work toward the research goal of this project. There will also be a certificate program on general plasma science for undergrad and graduate students, part of which will be lab training at Princeton University. Tier four will be the supervision and mentoring of Ph.D. students. Therefore, this project will systematically expand the talent pipeline, broaden participation from communities historically and geographically underrepresented in DOE SC research portfolio, significantly improve the research and education capacity at the PI’s institution, and contribute to developing a diverse workforce in plasma science and engineering.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Meshfree Methods

Meshfree methods have undergone substantial development and have received much attention in the last two decades. This new family of numerical methods is designed to inherit the main advantages of the finite element method such as compact supports of shape functions and good approximation properties while, at the same time, overcome the main disadvantages of the finite element method caused by the mesh dependence. The meshfree methods share a common feature that no mesh is needed and shape functions are constructed from sets of points, thus eliminating the need for time consuming mesh generation. The most significant advantage of meshfree methods is the flexibility in customizing approximation functions for desired regularity and for capturing essential physics and features of the particular problems of interest. Adaptivity formulation and multiple-scale solution strategies also can be implemented with relative ease. It has become clear that the meshfree methods provide considerable advantages over the conventional finite element methods in solving problems involving moving discontinuities, evolving material interfaces, multiple-scale phenomena, large material distortion and structural deformation, and fracture and damage processes. This Chapter gives an overview of many classes of meshfree methods, with more detailed discussions on Smoothed Particle Hydrodynamics (SPH), the Reproducing Kernel Particle Method (RKPM), Peridynamics (PD), the Material Point Method (MPM), as well as their applications in various challenging engineering problems.2

Chen, Jiun-Shyan↗

Evaluation of probability density function descriptions for three-component Rayleigh–Taylor mixing

Results from simulations of a three-component Rayleigh–Taylor (RT) mixing problem are presented. These simulations are conducted in heavy–light–heavy and heavy–intermediate–light configurations, and each of these configurations are further considered in high- and low-Reynolds-number regimes. This results in RT-unstable flow with one or both interfaces initially unstable, permitting the influence of problem configuration on the statistical description of three-component RT-driven mixing to be considered. Mass fraction covariances are observed to undergo a sign change through the mixing layer in all four configurations considered. This appears to be unique to the multi-component case and represents another way in which multi-component RT mixing differs from the two-component case. Qualitative and quantitative comparisons of joint and marginal probability density function (PDF) descriptions of species concentration are made. Three-, five-, and six-parameter model PDFs are compared against simulation data to assess how accurately they describe the mixing, and it is found that three-component mixing requires at least a five-parameter model PDF to accurately describe the mixing. Notably, the marginal distributions of three-component mixing do not appear to conform to a beta distribution, representing a departure from the classical two-component RT case. In conclusion, statistical neutrality also appears to influence the optimal choice of model PDF, which is found to be a function of problem configuration.

Large-eddy simulation↗

Non-Diffusive Volume Advection with A High Order Interface Reconstruction Method

We show that non-diffusive volume advection in two-dimensions is achieved with several benchmark problems using a newly developed high-order volume of fluids (VOF) interface reconstruction method. (1) A new VOF interface reconstruction method using circular/corner facets (linear facets are a degenerate case of arcs). We create a circular interface facet in each mixed zone by matching neighbor volume with a hybrid Newton’s-bisection method and the local solution is final. In the general case, the new VOF interface reconstruction has 3rd order accuracy and can be easily made seamless. The new method addresses intrinsic issues with Young’s method such as gaps between interface facets in the case of a curved interface, and inability to define curvature nor identify corners. (2) A non-diffusive volume advection scheme. In an ALE advection step, a well-defined interface can be carried over through a Lagrange step and used to compute volume distribution into a relaxed mesh. Then, an interface reconstruction step is performed to redefine the interface in the relaxed mesh. We must point out that the interface carried over is also a solution of interface reconstruction because all the volume fractions in the relaxed mesh are naturally matched. We provide an interface tracking method compatible with our reconstruction scheme, where it is granted to use the prior info as an initial guess to capture sub-mesh resolution features. As a result, we are able to treat multiple facets inside a single mixed cell and obtain highly accurate, non-diffusive solution for advection problems with rather coarse meshes. We show our solutions for two-dimensional incompressible flows with two materials with a) the X + O diagonal translation; b) the Zalesak rotational test; and c) the single vortex spiral test.

97 MATHEMATICS AND COMPUTING↗

Matching Crystal Structures Atom-to-Atom

Finding an optimal match between two different crystal structures underpins many important materials science problems, including describing solid-solid phase transitions and developing models for interface and grain boundary structures. Here, we formulate the matching of crystals as an optimization problem where the goal is to find the alignment and the atom-to-atom map that minimize a given cost function such as the Euclidean distance between the atoms. We construct an algorithm that directly solves this problem for large finite portions of the crystals and retrieves the periodicity of the match subsequently. We demonstrate its capacity to describe transformation pathways between known polymorphs and to reproduce experimentally realized structures of semi-coherent interfaces. Additionally, from our findings, we define a rigorous metric for measuring distances between crystal structures that can be used to properly quantify their geometric (Euclidean) closeness.

36 MATERIALS SCIENCE↗

Understanding and Advancing Bifacial Thin Film Solar Cells under Dual Illumination

There is a great deal of interest in increasing the energy yield from thin film solar cells by implementing bifacial operation. However, deleterious band bending and high interface recombination at the back transparent electrode can cause problems. Herein, it is investigated how bifacial thin film devices perform when illuminated through the front, back, and simultaneously through both interfaces using numerical modeling. It is shown that the downward band bending near the back interface is reduced during illumination when the carrier concentration is low. This effect is not found when the doping is relatively high, but the minority carrier distribution is still modified. Under either condition, the power generated under bifacial illumination exceeds the sum of the power generated when the illumination is solely from the back or the front. It is also shown that the back-illuminated device performance is independent of the angle at which the light enters the back of the device, which provides accommodation for scattered light. Finally, the power enhancement is calculated for bifacial devices relative to front-illuminated devices, and is shown that any significant loss in frontside power generation is difficult to overcome with back illumination under real-world albedo conditions.

CdTe↗

Designing interagency responses to wicked problems: A viable system model board game

Government agencies struggle to address wicked problems because they are open-ended, highly interdependent issues that cross agency, stakeholder, jurisdictional, and geopolitical boundaries. While both quantitative modelling and qualitative problem structuring methodologies have been used to support interagency decision making in the past, co-designing an effective interagency organization to collaboratively tackle wicked problems is more challenging. Few approaches have been developed to enable such efforts. This paper explains how the viable system model (VSM) was implemented through a board game, which was employed to co-design an interagency meta-organization that would be capable of more effectively collaborating to jointly address a wicked problem: international organized drug crime and its interface with local gangs in Chicago, USA. The board game was developed to make the VSM easier for the participants to learn, given that the cybernetic language and engineering-influenced diagrams in the original literature can be off-putting to leaders and managers. The board game was used as the final stage of a multi-method, systemic approach, which involved boundary critique and problem structuring as well as deployment of the VSM. The research findings indicate that the VSM board game, used as part of a larger mixed-methods systemic intervention, contributes to building trust in the value of systems thinking amongst the participants, and sets up a rich context for collaboration on multi-agency co-design. The game therefore offers significant promise as part of the co-design of interagency responses to wicked problems because it creates an embodied process for stakeholders to learn about the VSM. It also reduces the work involved in this learning. Thus, the game enables an effective appropriation of the VSM language and criteria.

Business & Economics↗

Optimization Plugin Library

The Optimization Plugin library ("op") is a lightweight general optimization solver interface. The primary purpose of op is to simplify the process of integrating different optimization solvers (serial or parallel) with scalable parallel physics engines. By design it has several features that help make this a reality. The core abstraction interface was developed to encompass a large class of optimization problems in an optimizer-agnostic way. This enables us to describe the optimization problem once and then use a variety of supported "op" optimizers with ideally no code-changes. The abstraction interface is made up of lightweight wrappers that make it easy to integrate with existing simulation codes. This makes integration less intrusive and should minimize changes to existing physics codes. The "op" interface includes an assortment of utility methods that help specify parallel communication patterns as well as methods to convert from optimization-specific interfaces to the more general "op" interface. Lastly a dynamic library linking interface is provided to allow for use of proprietary optimization engines without explicit reference in the source code, along with standard shared library interfaces for opensource engines.

Jekel, CharlesF↗

An MLIR-based Compiler Flow for System-Level Design and Hardware Acceleration

The generation of custom hardware accelerators for applications implemented within high-level productive programming frameworks requires considerable manual effort. To automate this process, we introduce \sodaopt, a compiler tool that extends the MLIR infrastructure. \sodaopt automatically searches, outlines, tiles, and pre-optimizes relevant code regions to generate high-quality accelerators through high-level synthesis. \sodaopt can support any high-level programming framework and domain-specific language that interface with the MLIR infrastructure. By leveraging MLIR, \sodaopt solves compiler optimization problems with specialized abstractions. Backend synthesis tools connect to \sodaopt through progressive intermediate representation lowerings. \sodaopt interfaces to a design space exploration engine to identify the combination of compiler optimization passes and options that provides high-performance generated designs for different backends and targets. We demonstrate the practical applicability of the compilation flow by exploring the automatic generation of accelerators for deep neural networks operators outlined at arbitrary granularity and by combining outlining with tiling on large convolution layers. Experimental results with kernels from the PolyBench benchmark show that \sodaopt high-level optimizations improve execution delays of synthesized accelerators up to 60x. We also show that for the selected kernels, our solution outperforms the current of state-of-the art in more than 70% of the benchmarks and provides better average speedup in 55% of them.

Bohm Agostini, Nicolas↗

Polysulfide-incompatible additive suppresses spatial reaction heterogeneity of Li-S batteries

Rational electrolyte engineering for practical pouch cells remains elusive because the correlation between the cathode/solid-electrolyte interphase layer and cell-level reaction behavior is poorly understood. Here, by combining multiscale characterization and computational modeling, we show that—counter to the conventional perception of polysulfide-incompatible additives—the spontaneous reaction of sparingly solvated polysulfides with Lewis acid additives (LAAs) can induce in situ formation of a homogeneous interphase on thick and tortuous S cathode. Multiscale synchrotron X-ray characterization consistently affirms that such interface design could effectively eliminate the notorious problems of polysulfide shuttle and lithium corrosion and, more importantly, provide an interconnected “ion transport highway” to alleviate the uneven ion transport within the tortuous S cathode. Hence, this design dramatically reduces the reaction heterogeneity of lithium-sulfur (Li-S) pouch cells under lean electrolyte conditions. Further, this work resolves controversy around the role of polysulfide-incompatible additives in high-energy Li-S pouch cells and highlights the importance of suppressing reaction heterogeneity for practical batteries.

36 MATERIALS SCIENCE↗

(U) LNK3DNT Capability in SENSMG Tested with Transport Correction

The SENSMG multigroup neutron sensitivity code can read materials and geometry from redoin and lnk3dnt files written by the PARTISN multigroup discrete ordinates code or the MCNP6 Monte Carlo code. Reference 5 described an initial version of this capability. Reference 6 introduced two important extensions: 1) Reaction-rate ratios are now allowed as responses with redoin/lnk3dnt inputs; and 2) Sensitivities of reaction-rate ratios to mass densities and interface locations are now calculated (for all problems, not just redoin/lnk3dnt problems). In this report, we document the testing of the redoin/lnk3dnt capability when used with transport correction. PARTISN’s transport corrections are described in Ref. 3, and Refs. 7 and 8 discuss the calculation of cross-section sensitivities when transport corrections are applied. References 7 and 8 verify SENSMG for problems with transport correction using central differences. This report verifies the capability with redoin/lnk3dnt inputs by comparison with regular SENSMG inputs. Unlike Refs. 5 and 6, in this report we use a spherical test problem because the sensitivity of the response with respect to the highest-order scattering is zero in cylinders due to the use of flux moments in the inner products.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

PyAlbany: A Python interface to the C++ multiphysics solver Albany

Albany is a parallel C++ finite element library for solving forward and inverse problems involving partial differential equations (PDEs). In this paper we introduce PyAlbany, a newly developed Python interface to the Albany library. PyAlbany can be used to effectively drive Albany enabling fast and easy analysis and post-processing of applications based on PDEs that are pre-implemented in Albany. PyAlbany relies on the library PyBind11 to bind Python with C++ Albany code. Here we detail the implementation of PyAlbany and showcase its capabilities through a number of examples targeting a heat-diffusion problem. In particular we consider the following: (1) the generation of samples for a Monte Carlo application, (2) a scalability study, (3) a study of parameters on the performance of a linear solver, and finally (4) a tool for performing eigenvalue decompositions of matrix-free operators for a Bayesian inference application.

97 MATHEMATICS AND COMPUTING↗