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DOE OSTI2021

SIERRA Multimechanics Module: Aria Thermal Theory Manual (V.5.2)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton’s method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic ℎ-adaptivity and dynamic load balancing are some of Aria’s more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria Thermal Theory Manual (V.5.4)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria User Manual (V.5.6)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( $Re$ < 1 ) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton's method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic $h$-adaptivity and dynamic load balancing are some of Aria's more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria Thermal Theory Manual (V.5.6)

Aria is a Galerkin nite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton’s method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic ℎ-adaptivity and dynamic load balancing are some of Aria’s more advanced capabilities.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria User Manual - Version 5.8

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria Thermal Theory Manual - Version 5.8

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process ows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton’s method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic ℎ-adaptivity and dynamic load balancing are some of Aria’s more advanced capabilities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria User Manual (V.5.10)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ($Re$ < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton’s method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic $h$-adaptivity and dynamic load balancing are some of Aria’s more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

SIERRA Multimechanics Module: Aria Thermal Theory Manual (V.5.10)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ($Re$ < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton’s method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic $h$-adaptivity and dynamic load balancing are some of Aria’s more advanced capabilities.

42 ENGINEERING↗

DOE OSTI2020

SIERRA Multimechanics Module: Aria Thermal Theory Manual (V.4.56)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton’s method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h -adaptivity and dynamic load balancing are some of Aria’s more advanced capabilities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Improved high-throughput screening technique to rapidly isolate Chlamydomonas transformants expressing recombinant proteins

Abstract The single-celled eukaryotic green alga Chlamydomonas reinhardtii has long been a model system for developing genetic tools for algae, and is also considered a potential platform for the production of high-value recombinant proteins. Identifying transformants with high levels of recombinant protein expression has been a challenge in this organism, as random integration of transgenes into the nuclear genome leads to low frequency of cell lines with high gene expression. Here, we describe the design of an optimized vector for the expression of recombinant proteins in Chlamydomonas , that when transformed and screened using a dual antibiotic selection, followed by screening using fluorescence activated cell sorting (FACS), permits rapid identification and isolation of microalgal transformants with high expression of a recombinant protein. This process greatly reduces the time required for the screening process, and can produce large populations of recombinant algae transformants with between 60 and 100% of cells producing the recombinant protein of interest, in as little as 3 weeks, that can then be used for whole population sequencing or individual clone analysis. Utilizing this new vector and high-throughput screening (HTS) process resulted in an order of magnitude improvement over existing methods, which normally produced under 1% of algae transformants expressing the protein of interest. This process can be applied to other algal strains and recombinant proteins to enhance screening efficiency, thereby speeding up the discovery and development of algal-derived recombinant protein products. Key points • A protein expression vector using double-antibiotic resistance genes was designed • Double antibiotic selection causes fewer colonies with more positive for phenotype • Coupling the new vector with FACS improves microalgal screening efficiency > 60%

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

SUNDIALS Multiphysics+MPIManyVector Performance Testing

In this report we document performance test results on a SUNDIALS-based multiphysics demonstration application. We aim to assess the large-scale parallel performance of new capabilities that have been added to the SUNDIALS suite of time integrators and nonlinear solvers in recent years under funding from both the Exascale Computing Project (ECP) and the Scientific Discovery through Advanced Scientific (SciDAC) program, specifically: 1. SUNDIALS’ new MPIManyVector module, that allows extreme flexibility in how a solution "vector" is staged on computational resources. 2. ARKode’s new multirate integration module, MRIStep, allowing high-order accurate calculations that subcycle "fast" processes within "slow" ones. 3. SUNDIALS’ new flexible linear solver interfaces, that allow streamlined specification of problem-specific linear solvers. 4. SUNDIALS’ new N_Vector additions of "fused" vector operations (to increase arithmetic intensity) and separation of reduction operations into "local" and "global" versions (to reduce latency by combining multiple reductions into a single MPI_Allreduce call). We anticipate that subsequent reports will extend this work to investigate a variety of other new features, including SUNDIALS’ generic SUNNonlinearSolver interface and accelerator-enabled N Vector modules, and upcoming MRIStep extensions to support custom "fast" integrators (that leverage problem structure) and IMEX integration of the "slow" time scale (to add diffusion).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Real-time chiral dynamics at finite temperature from quantum simulation

In this study, we explore the real-time dynamics of the chiral magnetic effect (CME) at a finite temperature in the (1+1)-dimensional QED, the massive Schwinger model. By introducing a chiral chemical potential μ 5 through a quench process, we drive the system out of equilibrium and analyze the induced vector currents and their evolution over time. The Hamiltonian is modified to include the time-dependent chiral chemical potential, thus allowing the investigation of the CME within a quantum computing framework. We employ the quantum imaginary time evolution (QITE) algorithm to study the thermal states, and utilize the Suzuki-Trotter decomposition for the real-time evolution. This study provides insights into the quantum simulation capabilities for modeling the CME and offers a pathway for studying chiral dynamics in low-dimensional quantum field theories.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Encoding of linear kinetic plasma problems in quantum circuits via data compression

We propose an algorithm for encoding linear kinetic plasma problems in quantum circuits. The focus is on modelling electrostatic linear waves in a one-dimensional Maxwellian electron plasma. The waves are described by the linearized Vlasov–Ampère system with a spatially localized external current that drives plasma oscillations. This system is formulated as a boundary-value problem and cast in the form of a linear vector equation Aψ = b to be solved by using the quantum signal processing algorithm. The latter requires encoding of matrix A in a quantum circuit as a sub-block of a unitary matrix. We propose how to encode A in a circuit in a compressed form and discuss how the resulting circuit scales with the problem size and the desired precision.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Generalized Theory and Realization of Reconfigurable Bandpass Filtering Equalizers

Here, in this article, a generalized theory of bandpass filtering equalizers is proposed. A filtering equalizer is a device that combines the frequency-selective properties of a filter with the controllable slope of an equalizer into a single component. The equations used to design the function for a desired slope are provided, and the design methodology to determine the necessary filtering polynomials is also shown. The controllable slope of the dual-function component is realized using variable capacitors, which are used to tune both a transmission zero and a matching network to achieve the desired slope. A third-order bandpass filtering equalizer is designed, fabricated, and measured to verify the generalized theory. The component is designed to operate at 1 GHz with a slope that can be reconfigured from 1 to 3 dB along the passband. This proposed filtering equalizer demonstrates the feasibility of a tunable, low-cost, size, weight, and power (C-SWaP) solution to enable increased flatness in the overall system response and thereby decrease the error vector magnitude (EVM) of future radio frequency (RF) systems and a design process that allows for future development of filtering equalizers.

Filter↗

DOE OSTI2020

Correlation-Aided Robust Decentralized Dynamic State Estimation of Power Systems with Unknown Control Inputs

This paper proposes a correlation-aided robust adaptive unscented Kalman filter for power system decentralized dynamic state estimation with unknown inputs, termed as robust AUKF-UI. The temporal and spatial correlations among the unknown inputs are used to derive a vector auto-regressive (VAR) model in an adaptive manner. This VAR model is further integrated together with state transition and measurement models for joint state and unknown inputs estimation. This allows taking into account the implicit cross-correlations between the states and the unknown inputs. As a result, the rank requirement for unknown input vector estimation is relaxed and the local generator frequency measurement is not required. The temporal correlations of time series innovation vectors, predicted state and input vectors are also leveraged by the robust AUKFUI to detect, identify and process bad data. Without these correlations, it is very challenging to address bad data with unknown inputs. Simulation results carried out on the IEEE 39-bus system demonstrate that the proposed robust AUKF-UI achieves much better results than other methods in the presence of low measurement redundancy, strong nonlinearity, and bad data.

Zhao, Junbo↗

DOE OSTI2022

A Study of QCD Radiation in VBF Higgs Production with Vincia and Pythia

We discuss and illustrate the properties of several parton-shower algorithms available in Pythia and Vincia, in the context of Higgs production via vector boson fusion (VBF). In particular, the distinctive colour topology of VBF processes allows to define observables sensitive to the coherent radiation pattern of additional jets. We study a set of such observables, using the Vincia sector-antenna shower as our main reference, and contrast it to Pythia's transverse-momentum-ordered DGLAP shower as well as Pythia's dipole-improved shower. We then investigate the robustness of these predictions as successive levels of higher-order perturbative matrix elements are incorporated, including next-to-leading-order matched and tree-level merged calculations, using Powheg Box and Sherpa respectively to generate the hard events.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Hadron spectroscopy of pseudoscalar and vector meson photoproduction using linearly polarised photons at CLAS

The field of hadron spectroscopy is informed by experiments which study excited states of the nucleon by detecting the decay products following excitation with a hadronic, leptonic or electromagnetic probe. Experiments using a polarised beam of photons provide an important contribution to the world data. This thesis describes the analysis of data from one such experiment, the CEBAF Large Acceptance Spectrometer at Jefferson Laboratory, Virginia, USA. In the experiment, an incident beam of electrons passes through a diamond radiator producing a linearly polarised photon beam of energy from 1.1 to 2.1 GeV on a liquid hydrogen target. The analysis method and results for two reaction channels are presented. In the first analysis, the polarisation observables {?, P, T, Ox, Oz} for the reaction ??? p ? K0 S ?+ are extracted simultaneously using likelihood sampling with Markov-Chain Monte-Carlo. The results are presented as angular distributions (cos ?K0S) for bins in photon energy E? for a total of 21 bins. The values extracted for T , Ox and Oz are a first measurement of these quantities for this reaction and the beam asymmetry (?) measurement supplements the one previous measurement for this quantity and extends the energy range over which it has been extracted. The measurement of the recoil polarisation, P, is consistent with previous measurements. In a second analysis, the spin density matrix elements (SDMEs) for ? p ? p ? are extracted using similar analysis techniques. The results are presented as angular distributions (cos ?? ) for bins in photon energy E? for a total of 24 bins. This work is the first to extract all nine SDMEs for the full angular range of the ? meson production. A comparison is made to the predictions of the Vector Meson Dominance (VMD) model and the results provide evidence for contributing processes other than VMD, particularly at more backward angles of the ? meson production. The data also indicate non-helicity conserving process in both the s-channel and the t-channel. The results from the first analysis have been passed to the Juelich-Bonn theory group and the effect of including the new data within their dynamical coupled channel model is described. Several nucleon resonances are affected and the impact on the pole positions, widths and photon decay amplitudes of the affected resonances is described.

Clark, Louise↗

DOE OSTI2022

Cryo-electron Microscopy of Adeno-associated Virus

Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.

59 BASIC BIOLOGICAL SCIENCES↗