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At least 181 records · Page 10

Dual-map framework for noise characterization of quantum computers

In order to understand the capabilities and limitations of quantum computers, it is necessary to develop methods that efficiently characterize and benchmark error channels present on these devices. In this paper, we present a method that faithfully reconstructs a marginal (local) approximation of the effective noise (MATEN) channel, that acts as a single layer at the end of the circuit. We first introduce a dual-map framework that allows us to analytically derive expectation values of observables with respect to noisy circuits. These findings are supported by numerical simulations of the quantum approximate optimization algorithm (QAOA) that also justify the MATEN, even in the presence of nonlocal errors that occur during a circuit. Finally, we demonstrate the performance of the method on Rigetti's Aspen-11 quantum computer for QAOA circuits up to six qubits, successfully predicting the observed measurements on a majority of the qubits.

Sud, James↗

Computational design of thermoelectric alloys through optimization of transport and dopability

Alloying is a common technique to optimize the functional properties of materials for thermoelectrics, photovoltaics, energy storage etc. Designing thermoelectric (TE) alloys is especially challenging because it is a multi-property optimization problem, where the properties that contribute to high TE performance are interdependent. In this work, we develop a computational framework that combines first-principles calculations with alloy and point defect modeling to identify alloy compositions that optimize the electronic, thermal, and defect properties. We apply this framework to design n-type Ba 2(1–x) Sr 2x CdP 2 Zintl thermoelectric alloys. Our predictions of the crystallographic properties such as lattice parameters and site disorder are validated with experiments. To optimize the conduction band electronic structure, we perform band unfolding to sketch the effective band structures of alloys and find a range of compositions that facilitate band convergence and minimize alloy scattering of electrons. Here, we assess the n-type dopability of the alloys by extending the standard approach for computing point defect energetics in ordered structures. Through the application of this framework, we identify an optimal alloy composition range with the desired electronic and thermal transport properties, and n-type dopability. Such a computational framework can also be used to design alloys for other functional applications beyond TE.

36 MATERIALS SCIENCE↗

A bidirectional coupling procedure applied to multiscale respiratory modeling

In this study, we present a novel multiscale computational framework for efficiently linking multiple lower-dimensional models describing the distal lung mechanics to imaging-based 3D computational fluid dynamics (CFDs) models of the upper pulmonary airways in order to incorporate physiologically appropriate outlet boundary conditions. The framework is an extension of the modified Newton’s method with nonlinear Krylov accelerator developed by Carlson and Miller [1], Miller [2] and Scott and Fenves [3]. Our extensions include the retention of subspace information over multiple timesteps, and a special correction at the end of a timestep that allows for corrections to be accepted with verified low residual with as little as a single residual evaluation per timestep on average. In the case of a single residual evaluation per timestep, the method has zero additional computational cost compared to uncoupled or unidirectionally coupled simulations. We expect these enhancements to be generally applicable to other multiscale coupling applications where timestepping occurs. In addition we have developed a “pressure-drop” residual which allows for stable coupling of flows between a 3D incompressible CFD application and another (lower-dimensional) fluid system. We expect this residual to also be useful for coupling non-respiratory incompressible fluid applications, such as multiscale simulations involving blood flow. The lower-dimensional models that are considered in this study are sets of simple ordinary differential equations (ODEs) representing the compliant mechanics of symmetric human pulmonary airway trees. To validate the method, we compare the predictions of hybrid CFD–ODE models against an ODE-only model of pulmonary airflow in an idealized geometry. Subsequently, we couple multiple sets of ODEs describing the distal lung to an imaging-based human lung geometry. Boundary conditions in these models consist of atmospheric pressure at the mouth and intrapleural pressure applied to the multiple sets of ODEs. In both the simplified geometry and in the imaging-based geometry, the performance of the method was comparable to that of monolithic schemes, in most cases requiring only a single CFD evaluation per time step. Thus, this new accelerator allows us to begin combining pulmonary CFD models with lower-dimensional models of pulmonary mechanics with little computational overhead. Moreover, because the CFD and lower-dimensional models are totally separate, this framework affords great flexibility in terms of the type and breadth of the adopted lower-dimensional model, allowing the biomedical researcher to appropriately focus on model design. Research funded by the National Heart and Blood Institute Award 1RO1HL073598.

60 APPLIED LIFE SCIENCES↗

Feedback-based quantum algorithms for ground state preparation

The ground state properties of quantum many-body systems are a subject of interest across chemistry, materials science, and physics. Thus, algorithms for finding ground states can have broad impacts. Variational quantum algorithms are one class of ground state algorithms that has received significant attention in recent years. These algorithms utilize a hybrid quantum-classical computing framework to prepare ground states on quantum computers. However, this requires solving a classical optimization problem that can become prohibitively expensive in high dimensions. Here, we develop formulations of feedback-based quantum algorithms for ground state preparation that can be used to address this challenge for two broad classes of Hamiltonians: Fermi-Hubbard Hamiltonians, and molecular Hamiltonians represented in second quantization. Feedback-based quantum algorithms are optimization-free; in place of classical optimization, quantum circuit parameters are set according to a deterministic feedback law derived from quantum Lyapunov control principles. This feedback law guarantees a monotonic improvement in solution quality with respect to the depth of the quantum circuit. A variety of numerical illustrations are provided that analyze the convergence and robustness of feedback-based quantum algorithms for these problem classes. Published by the American Physical Society 2024

Larsen, James B. (ORCID:000000020777440X)↗

An Eulerian crystal plasticity framework for modeling large anisotropic deformations in energetic materials under shocks

Here, this paper demonstrates a novel Eulerian computational framework for modeling anisotropic elastoplastic deformations of organic crystalline energetic materials (EM) under shocks. While Eulerian formulations are advantageous for handling large deformations, constitutive laws in such formulations have been limited to isotropic elastoplastic models, which may not fully capture the shock response of crystalline EM. The present Eulerian framework for high-strain rates, large deformation material dynamics of EM incorporates anisotropic isochoric elasticity via a hypo-elastic constitutive law and visco-plastic single-crystal models. The calculations are validated against atomistic calculations and experimental data and benchmarked against Lagrangian (finite element) crystal plasticity computations for shock-propagation in a monoclinic organic crystal, octahydro-1,3,5,7-tetranitro-1,3,5,7 tetrazocine (β-HMX). The Cauchy stress components and the resolved shear stresses calculated using the present Eulerian approach are shown to be in good agreement with the Lagrangian computations for different crystal orientations. The Eulerian framework is then used for computations of shock-induced inert void collapse in β-HMX to study the effects of crystal orientations on hotspot formation under different loading intensities. The computations show that the hotspot temperature distributions and the collapse profiles are sensitive to the crystal orientations at lower impact velocities (viz., 500 m/s); when the impact velocity is increased to 1000 m/s, the collapse is predominantly hydrodynamic and the role of anisotropy is modest. The present methodology will be useful to simulate energy localization in shocked porous energetic material microstructures and other situations where large deformations of single and polycrystals govern the thermomechanical response.

42 ENGINEERING↗

A mathematical framework for thermodynamic computing with applications to chemical reaction networks

The widespread adoption of energy-intensive computing applications has led to a growing need for energy-efficient computing approaches. Thermodynamic computing offers a promising approach for low-energy computation by leveraging the intrinsic computational capabilities of physical, chemical, or biological systems. However, the mathematical foundations of thermodynamic computing require further development to fully realize the potential energy efficiencies, as well as to assess factors like noise and operational speed. In this paper, we establish a mathematical framework for utilizing thermodynamic processes to perform fundamental operations, including addition, subtraction, multiplication, and division. We highlight the use of chemical reactions as potential computational units and explore synthetic chemical and biochemical systems as practical implementations. Additionally, we demonstrate how these principles can be applied to solving complex mathematical problems, such as ordinary differential equations (ODEs) and suggest the necessary components to implement the thermodynamic computing framework using chemical reactions based in a microfluidic device. This work enhances our understanding of thermodynamic processes for natural computing as a basis for scalable, energy-efficient computation in paradigm disruptive next-generation systems.

Cannon, William R. [Pacific Northwest National Lab↗

Discovery of hybrid chemical synthesis pathways with DORAnet

Developing efficient tools for discovering novel synthesis pathways is essential to advance chemical production methods that maximize the use of resources and energy. We introduce DORAnet (Designing Optimal Reaction Avenues Network Enumeration Tool), an open-source computational framework that addresses key limitations in current computer-aided synthesis planning (CASP) tools. DORAnet integrates both chemical/chemocatalytic (i.e., non-enzymatic) and enzymatic transformations, enabling the discovery of hybrid synthesis pathways. With 390 expert-curated chemical/chemocatalytic reaction rules and 3606 enzymatic rules derived from MetaCyc, it provides extensive flexibility for synthetic chemists and biotechnologists. The framework features customizable network expansion strategies, advanced filtering, and pathway search, ranking, and visualization tools. Validated against known reaction data, DORAnet successfully identified both established and novel synthesis routes for key industrial chemicals. In a case study involving 51 high-volume targets, DORAnet frequently ranked known commercial pathways among the top three results, demonstrating its practical relevance and ranking accuracy, while also uncovering numerous alternative (hybrid) synthesis pathways that were highly ranked.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

End-to-end AI framework for interpretable prediction of molecular and crystal properties

We introduce an end-to-end computational framework that allows for hyperparameter optimization using the DeepHyper library, accelerated model training, and interpretable AI inference. The framework is based on state-of-the-art AI models including CGCNN, PhysNet, SchNet, MPNN, MPNN-transformer, and TorchMD-NET. We employ these AI models along with the benchmark QM9, hMOF, and MD17 datasets to showcase how the models can predict user-specified material properties within modern computing environments. We demonstrate transferable applications in the modeling of small molecules, inorganic crystals and nanoporous metal organic frameworks with a unified, standalone framework. We have deployed and tested this framework in the ThetaGPU supercomputer at the Argonne Leadership Computing Facility, and in the Delta supercomputer at the National Center for Supercomputing Applications to provide researchers with modern tools to conduct accelerated AI-driven discovery in leadership-class computing environments. We release these digital assets as open source scientific software in GitLab, and ready-to-use Jupyter notebooks in Google Colab.

36 MATERIALS SCIENCE↗

A coupled discontinuous Galerkin-Finite Volume framework for solving gas dynamics over embedded geometries

Herein, we present a computational framework for solving the equations of inviscid gas dynamics using structured grids with embedded geometries. The novelty of the proposed approach is the use of high-order discontinuous Galerkin (dG) schemes and a shock-capturing Finite Volume (FV) scheme coupled via an hp adaptive mesh refinement (hp-AMR) strategy that offers high-order accurate resolution of the embedded geometries. The hp-AMR strategy is based on a multi-level block-structured domain partition in which each level is represented by block-structured Cartesian grids and the embedded geometry is represented implicitly by a level set function. The intersection of the embedded geometry with the grids produces the implicitly-defined mesh that consists of a collection of regular rectangular cells plus a relatively small number of irregular curved elements in the vicinity of the embedded boundaries. High-order quadrature rules for implicitly-defined domains enable high-order accuracy resolution of the curved elements with a cell-merging strategy to address the small-cell problem. The hp-AMR algorithm treats the system with a second-order finite volume scheme at the finest level to dynamically track the evolution of solution discontinuities while using dG schemes at coarser levels to provide high-order accuracy in smooth regions of the flow. On the dG levels, the methodology supports different orders of basis functions on different levels. The space-discretized governing equations are then advanced explicitly in time using high-order Runge-Kutta algorithms. Numerical tests are presented for two-dimensional and three-dimensional problems involving an ideal gas. The results are compared with both analytical solutions and experimental observations and demonstrate that the framework provides high-order accuracy for smooth flows and accurately captures solution discontinuities.

97 MATHEMATICS AND COMPUTING↗

Applications of Deep Learning to physics workflows

Modern large-scale physics experiments create datasets with sizes and streaming rates that can exceed those from industry leaders such as Google Cloud and Netflix. Fully processing these datasets requires both sufficient compute power and efficient workflows. Recent advances in Machine Learning (ML) and Artificial Intelligence (AI) can either improve or replace existing domain-specific algorithms to increase workflow efficiency. Not only can these algorithms improve the physics performance of current algorithms, but they can often be executed more quickly, especially when run on coprocessors such as GPUs or FPGAs. In the winter of 2023, MIT hosted the Accelerating Physics with ML at MIT workshop, which brought together researchers from gravitational-wave physics, multi-messenger astrophysics, and particle physics to discuss and share current efforts to integrate ML tools into their workflows. The following white paper highlights examples of algorithms and computing frameworks discussed during this workshop and summarizes the expected computing needs for the immediate future of the involved fields.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Data and Model-Driven Decision Support for Environmental Management of a Chromium Plume at Los Alamos National Laboratory - 13264

A series of site investigations and decision-support analyses have been performed related to a chromium plume in the regional aquifer beneath the Los Alamos National Laboratory (LANL). Based on the collected data and site information, alternative conceptual and numerical models representing governing subsurface processes with different complexity and resolution have been developed. The current conceptual model is supported by multiple lines of evidence based on comprehensive analyses of the available data and modeling results. The model is applied for decision-support analyses related to estimation of contaminant- arrival locations and chromium mass flux reaching the regional aquifer, and to optimization of a site monitoring-well network. Plume characterization is a challenging and non-unique problem because multiple models and contamination scenarios are consistent with the site data and conceptual knowledge. To solve this complex problem, an advanced methodology based on model calibration and uncertainty quantification has been developed within the computational framework MADS (http://mads.lanl.gov). This work implements high-performance computing and novel, efficient and robust model analysis techniques for optimization and uncertainty quantification (ABAGUS, Squads, multi-try (multi-start) techniques), which allow for solving problems with large degrees of freedom. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

PvaPy streaming framework for real-time data processing

User facility upgrades, new measurement techniques, advances in data analysis algorithms as well as advances in detector capabilities result in an increasing amount of data collected at X-ray beamlines. Some of these data must be analyzed and reconstructed on demand to help execute experiments dynamically and modify them in real time. In turn, this requires a computing framework for real-time processing capable of moving data quickly from the detector to local or remote computing resources, processing data, and returning results to users. In this paper, we discuss the streaming framework built on top of PvaPy, a Python API for the EPICS pvAccess protocol. We describe the framework architecture and capabilities, and discuss scientific use cases and applications that benefit from streaming workflows implemented on top of this framework. We also illustrate the framework's performance in terms of achievable data-processing rates for various detector image sizes.

EPICS pvAccess↗

Trigger-based Incremental Data Processing with Unified Sync and Async Model

In recent years, more and more applications in the cloud have needs to process large-scale on-line datasets, which evolve over time as new entries are added and existing entries are modified. Several programming frameworks, such as Percolator and Oolong, are proposed for such incremental data processing and can achieve efficient processing with an event-driven abstraction. However, these frameworks are inherently asynchronous, leaving the heavy burden of managing synchronization to applications' developers, which further significantly restricts their usabilities. In this study, we propose a trigger-based incremental computing framework in the cloud, called Domino, with both synchronous and asynchronous mechanisms to coordinate parallel triggers. With this new framework, both synchronous and asynchronous applications can be seamlessly developed. Use cases and extensive evaluation results confirm that it can deliver sufficient performance, and also is easy to use for incremental applications in large-scale distributed computing.

97 MATHEMATICS AND COMPUTING↗

An analytical method as a preconditioning modeling for systems of linear equations

In this paper, we propose a simple and practical preconditioner based on the homotopy analysis method. Furthermore, using this modeling, we design an efficient algorithm to solve linear systems. Within the computational framework, convection–diffusion equation candidates are investigated and evaluated. Finally, computational comparisons of the standard methods against preconditioned methods based on experiments are presented which illustrate the merits of the simplicity, power, and effectiveness of the proposed algorithm.

97 MATHEMATICS AND COMPUTING↗

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↗

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

Background: There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. Results: This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. Conclusions: In this paper, we presented a highly scalable and efficient genome assembly software, SWAPAssembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler

59 BASIC BIOLOGICAL SCIENCES↗

Integrated edge-to-exascale workflow for real-time steering in neutron scattering experiments

We introduce a computational framework that integrates artificial intelligence (AI), machine learning, and high-performance computing to enable real-time steering of neutron scattering experiments using an edge-to-exascale workflow. Focusing on time-of-flight neutron event data at the Spallation Neutron Source, our approach combines temporal processing of four-dimensional neutron event data with predictive modeling for multidimensional crystallography. At the core of this workflow is the Temporal Fusion Transformer model, which provides voxel-level precision in predicting 3D neutron scattering patterns. The system incorporates edge computing for rapid data preprocessing and exascale computing via the Frontier supercomputer for large-scale AI model training, enabling adaptive, data-driven decisions during experiments. This framework optimizes neutron beam time, improves experimental accuracy, and lays the foundation for automation in neutron scattering. Although real-time experiment steering is still in the proof-of-concept stage, the demonstrated potential of this system offers a substantial reduction in data processing time from hours to minutes via distributed training, and significant improvements in model accuracy, setting the stage for widespread adoption across neutron scattering facilities and more efficient exploration of complex material systems.

97 MATHEMATICS AND COMPUTING↗

Strain localization in dry sheared granular materials: A compactivity-based approach

Shear banding is widely observed in natural fault zones as well as in laboratory experiments on granular materials. Understanding the dynamics of strain localization under different loading conditions is essential for quantifying strength evolution of fault gouge, energy partitioning during earthquakes and characterizing rheological transitions and fault zone structure changes. To that end, we develop a physics-based continuum model for strain localization in sheared granular materials. The grain-scale dynamics is described by the Shear Transformation Zone (STZ) theory, a non-equilibrium statistical thermodynamic framework for viscoplastic deformation in amorphous materials. Using a finite strain computational framework, we investigate the initiation and growth of complex shear bands under a variety of loading conditions and identify implication for strength evolution and ductile to brittle transition. Our numerical results show similar localization patterns to field and lab observations and suggest that shear zones show more ductile response at higher confining pressures, lower dilatancy and loose initial conditions. Lower pressures, higher dilatancy and dense initial conditions favor a brittle response and larger strength drops. These findings shed light on a range of mechanisms for strength evolution in dry sheared granular materials and provide a critical input to physicsbased multiscale models of fault zone instabilities.

36 MATERIALS SCIENCE↗