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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

On-lattice kinetic Monte Carlo approaches for modeling molecular anisotropy in resveratrol crystallization

Stilbenes are a class of organic compounds with broad-ranging pharmaceutical and agricultural applications, which are typically isolated and purified through recrystallization. We are motivated by reducing experimental waste and optimizing yield via developing predictive simulations for processing-dependent crystal morphologies. Using resveratrol as a model stilbene system, we have developed an approach for simulating crystallization with molecular resolution using on-lattice kinetic Monte Carlo. In this work, we highlight modifications to the Stochastic Parallel PARticle Kinetic Simulator (SPPARKS) software package, which were essential to this application. Key enhancements include the incorporation of non-orthogonal cell shapes and monomer anisotropy approximations using bound hard spheres. This new SPPARKS application has been applied to resveratrol with attachment energy libraries obtained from density functional theory, resulting in excellent agreement with experimental morphology prediction.

crystallization↗
DOE OSTI2022

Atomic-resolution lithography with an on-chip scanning tunneling microscope

In this work, atomic-resolution lithography with a Microelectromechanical-System (MEMS) based Scanning Tunneling Microscope (STM) is demonstrated for the first time. The microscope consists of a commercial UltraHigh-Vacuum (UHV) STM whose regular tip is replaced with a 1-Degree-of-Freedom (1-DOF) MEMS nanopositioner. This results in a hybrid STM system where XY-plane motions are provided by the piezotube of the original system and Z-axis motion by the MEMS with a higher bandwidth. Sharp tips made of Pt or W are added to the MEMS devices with postfabrication techniques. With this hybrid system, STM-based lithography is demonstrated on an H-passivated Si (100)-2×1 sample under UHV condition. Results prove the capability of the hybrid STM system for atomic-scale lithography. This capability, paired with the small footprint of the MEMS device, makes this approach a candidate for building a high-throughput parallel STM lithography platform by incorporating an array of 1-DOF MEMS devices that perform lithography in parallel.

Alipour, Afshin (ORCID:0000000263252067)↗
DOE OSTI2021

YAHFC: A Code Framework to Model Nuclear Reactions and Estimate Correlated Uncertainties

Reaction modeling is a key ingredient in designing experiments and interpreting their results, and is an essential component in the process of evaluating nuclear data and assembling nuclear data libraries used in nuclear technology applications. Typically, experimental data are available only for a handful of reaction channels and theory models are used to fill in the gaps. In addition, theory is often called upon as the arbitrator between discrepant data. Most importantly, theory and modeling are required for an accurate determination of uncertainties in the evaluated data and the correlations between the multiple channels. A fast, accurate, and flexible modeling capability has been developed at LLNL with the code system YAHFC (Yet Another Hauser-Feshbach Code). YAHFC is a Monte Carlo, Hauser-Feshbach code framework, making full use of dynamic memory allocation, derived types, and parallel computing. YAHFC can generate events to simulate experiments and is guiding experiments designed to measure inelastic neutron scattering from actinide targets. YAHFC is also being used to analyze decays from surrogate experiments, thereby enabling the inference of reaction cross sections inaccessible by direct measurement. Finally, by modeling nuclear reactions with constraints from experimental data, YAHFC can deliver complete nuclear data libraries, with evaluated uncertainties, using the modernized Generalized Nuclear Data Structure (GNDS).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Stability analysis of a one-dimensional multiphysics model of a molten salt fast reactor

Reactor designs with a fast neutron spectrum have recently moved into the research focus for possible Generation IV reactor concepts - a representative of which is the molten salt fast reactor (MSFR). In order to assess the safety and reliability of this reactor concept, it is necessary to obtain knowledge of the system behaviour. An important part of this research concerns the dynamical stability of the MSFR. Research regarding the MSFR stability so far has either been using linearized models for stability criteria or only been examining certain transients at fixed parameter values. This work delivers a comprehensive stability analysis for a non-linearized MSFR model, and a wide range of values for all relevant parameters. For this purpose, a one-dimensional MSFR model was set up, taking neutron kinetics and thermal hydraulics in the form of a system of differential equations into account. The stability of this model was investigated by means of the numerical tool MATCONT, which was used to monitor the evolution of a so-called fixed-point solution, here referring to the steady state at operating conditions of the system, while system parameters got varied. The MATCONT analyses showed no loss of stability for any of the considered parameter variations and no solutions that might co-exist in parallel with the steady-state fixed-point solution. Therefore these results indicate a stable fixed point to which all solution transients converge, making the considered MSFR model insusceptible to deviations from the equilibrium. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Discovery of Extended Tidal Tails around the Globular Cluster Palomar 13

We use photometry from the DECam Legacy Survey to detect candidate tidal tails extending ~5° on either side of the Palomar 13 globular cluster. The tails are aligned with the proper motion of Palomar 13 and are consistent with its old, metal-poor stellar population. We identify three RR Lyrae stars (RRLs) that are plausibly associated with the tails, in addition to four previously known in the cluster. From these RRLs, we find that the mean distance to the cluster and tails is 23.6 ± 0.2 kpc and estimate the total (initial) luminosity of the cluster to be , consistent with previous claims that its initial luminosity was higher than its current luminosity. Combined with previously determined proper motion and radial velocity measurements of the cluster, we find that Palomar 13 is on a highly eccentric orbit (e ~ 0.8) with a pericenter of ~9 kpc and an apocenter of ~69 kpc, and a recent pericentric passage of the cluster ~75 Myr ago. We note a prominent linear structure in the interstellar dust map that runs parallel to the candidate tidal features, but conclude that reddening due to dust is unlikely to account for the structure that we observe. If confirmed, the Palomar 13 stellar stream would be one of very few streams with a known progenitor system, making it uniquely powerful for studying the disruption of globular clusters, the formation of the stellar halo, and the distribution of matter within our Galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Resiliency in numerical algorithm design for extreme scale simulations

Here this work is based on the seminar titled ‘Resiliency in Numerical Algorithm Design for Extreme Scale Simulations’ held March 1–6, 2020, at Schloss Dagstuhl, that was attended by all the authors. Advanced supercomputing is characterized by very high computation speeds at the cost of involving an enormous amount of resources and costs. A typical large-scale computation running for 48 h on a system consuming 20 MW, as predicted for exascale systems, would consume a million kWh, corresponding to about 100k Euro in energy cost for executing 10 23 floating-point operations. It is clearly unacceptable to lose the whole computation if any of the several million parallel processes fails during the execution. Moreover, if a single operation suffers from a bit-flip error, should the whole computation be declared invalid? What about the notion of reproducibility itself: should this core paradigm of science be revised and refined for results that are obtained by large-scale simulation? Naive versions of conventional resilience techniques will not scale to the exascale regime: with a main memory footprint of tens of Petabytes, synchronously writing checkpoint data all the way to background storage at frequent intervals will create intolerable overheads in runtime and energy consumption. Forecasts show that the mean time between failures could be lower than the time to recover from such a checkpoint, so that large calculations at scale might not make any progress if robust alternatives are not investigated. More advanced resilience techniques must be devised. The key may lie in exploiting both advanced system features as well as specific application knowledge. Research will face two essential questions: (1) what are the reliability requirements for a particular computation and (2) how do we best design the algorithms and software to meet these requirements? While the analysis of use cases can help understand the particular reliability requirements, the construction of remedies is currently wide open. One avenue would be to refine and improve on system- or application-level checkpointing and rollback strategies in the case an error is detected. Developers might use fault notification interfaces and flexible runtime systems to respond to node failures in an application-dependent fashion. Novel numerical algorithms or more stochastic computational approaches may be required to meet accuracy requirements in the face of undetectable soft errors. These ideas constituted an essential topic of the seminar. The goal of this Dagstuhl Seminar was to bring together a diverse group of scientists with expertise in exascale computing to discuss novel ways to make applications resilient against detected and undetected faults. In particular, participants explored the role that algorithms and applications play in the holistic approach needed to tackle this challenge. This article gathers a broad range of perspectives on the role of algorithms, applications and systems in achieving resilience for extreme scale simulations. The ultimate goal is to spark novel ideas and encourage the development of concrete solutions for achieving such resilience holistically.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

HIPLZ: Enabling performance portability for exascale systems

While heterogeneous computing has emerged as a dominant trend in current and future High-Performance Computing (HPC) systems, it is also widely recognized that this shift has led to increased software complexity due to a proliferation of programming systems for different heterogeneous processors. One such example is the Heterogeneous-Compute Interface for Portability from AMD (HIP ), which is composed of a C Runtime API and C++ Kernel Language. Many HPC applications will likely use HIP on future exascale systems (e.g., Frontier and El Capitan), but HIP currently only targets AMD and NVIDIA processors. This limitation creates challenges for users who would also like to run their applications on exascale systems based on other architectures (e.g., Aurora, which is based on Intel hardware) that are currently not targeted by HIP . In this paper, we introduce the design and implementation of HIPLZ , a compiler and runtime system that uses the Intel Level Zero API to support HIP on Intel GPU architectures. We discuss the design of HIPLZ , derived from HIPCL (an implementation of HIP on top of OpenCL ), and portability issues that occur from using the Level Zero runtime as a backend. We evaluate our implementation by running several performance benchmarks and mini-apps written in HIP on Intel architectures using HIPLZ . Our results show that this approach provides competitive performance relative to Intel's OpenCL implementations on Intel Gen9 and UHD Graphics 770 GPUs, while providing good coverage of features needed by HPC applications. Overall, this approach is a promising demonstration of enabling performance portability for exascale systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons

Abstract Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Progress in ITER ECE diagnostic design and integration

The ITER electron cyclotron emission (ECE) diagnostic system has primary roles in providing measurements of the core electron temperature profile and the electron temperature fluctuation associated with the neoclassical tearing modes. The ITER ECE system includes a radial and oblique line-of-sight. Four 43-meter long low-loss transmission lines (TLs) are designed to transmit millimeter wave power in the frequency range of 70–1000 GHz in both X- and O-mode polarization from the port plug to the ECE instrumentation room in the diagnostic building. The measurement instrumentation includes two Fourier transform spectrometer (FTS) systems and two radiometer systems. The Indian Domestic Agency (IN-DA) and United States Domestic Agency share the responsibility. The IN-DA scope excluding instrumentation and control has passed its preliminary design review and is progressing towards the final design review (FDR). In parallel, the diagnostic integration in different areas is ongoing. Furthermore, several captive components for the TLs have passed FDR and will be manufactured for installation in the tokamak building soon. A peer review meeting has been held on the prototype hot calibration source, and its integration and new thermal analysis in the diagnostic shield module are continuing. A prototype TL is being tested. A prototype polarizing Martin-Puplett type FTS, operating in the frequency range 70–1000 GHz, features an in-vacuo fast scanning mechanism and a cryo-cooled dual-channel THz detector system. Its performance has been assessed in detail against ITER requirements.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Graph-based quantum response theory and shadow Born–Oppenheimer molecular dynamics

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born–Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. Further, the proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Unusual Quasiparticles and Tunneling Conductance in Quantum Point Contacts in 𝜈 = 2/3 Fractional Quantum Hall Systems

Understanding topological matter in the fractional quantum Hall (FQH) effect requires identifying the nature of edge state quasiparticles. FQH edge state at the filling factor 𝜈 = 2/3 in the spin-polarized and unpolarized phases is represented by the two modes of composite fermions (CF) with the parallel or opposite spins described by the chiral Luttinger liquids. Tunneling through a quantum point contact (QPC) between different or similar spin phases is solved exactly. With the increase of the applied voltage, the QPC conductance grows from zero and saturates at 𝑒 2 /2⁢ℎ while a weak electron tunneling between the edge modes with the same spin transforms into a backscattering carried by the charge 𝑞 = 𝑒/2 quasiparticles. These unusual quasiparticles and conductance plateau emerge when one or two CF spin-polarized modes in the QPC tunnel into a single mode. Here, we propose experiments on the applied voltage and temperature dependence of the QPC conductance and noise that can shed light on the nature of edge states and FQH transport.

Anyons↗
DOE OSTI2024

Entanglement Renormalization for Quantum Field Theories with Discrete Wavelet Transforms

We propose an adaptation of Entanglement Renormalization for quantum field theories that, through the use of discrete wavelet transforms, strongly parallels the tensor network architecture of the Multiscale Entanglement Renormalization Ansatz (a.k.a. MERA). Our approach, called wMERA, has several advantages of over previous attempts to adapt MERA to continuum systems. In particular, (i) wMERA is formulated directly in position space, hence preserving the quasi-locality and sparsity of entanglers; and (ii) it enables a built-in RG flow in the implementation of real-time evolution and in computations of correlation functions, which is key for efficient numerical implementations. As examples, we describe in detail two concrete implementations of our wMERA algorithm for free scalar and fermionic theories in (1+1) spacetime dimensions. Possible avenues for constructing wMERAs for interacting field theories are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Behavior of soda-lime silicate glass under laser-driven shock compression up to 315 GPa

Shock experiments give a unique insight into the behavior of matter subjected to extremely high pressures and temperatures. Understanding the behavior of materials under such extreme conditions is key to modeling material failure and deformation dynamics under impact. While studies on pure silica are extensive, the shock behavior of other commercial silicates that contain additional oxides has not been systematically investigated. To better understand the role of composition in the dynamic behavior of silicates, we performed laser-driven dynamic compression experiments on soda-lime glass (SLG) up to 315 GPa. Using the accurate pulse shaping offered by the long pulse laser system at the Matter in Extreme Conditions end-station at the Linac Coherent Light Source, SLG was shock compressed along the Hugoniot to multiple pressure-temperature points. Velocity Interferometer System for Any Reflector was used to measure the velocity and determine the pressure inside the SLG. The U s –u p relationship obtained agrees well with the previous parallel plate impact studies. Within the error bars, no transformation to the crystalline phase was observed up to 70 GPa, which is in contrast to the behavior of pure silica under shock compression. Our studies show that the glass composition strongly influences the shock compression behavior of the silicate glasses.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Review of solar-enabled desalination and implications for zero-liquid-discharge applications

Abstract The production of freshwater from desalinating abundant saline water on the planet is increasingly considered a climate change adaptation measure. Yet, there are challenges associated with the high cost, intensive energy demand, and environmental implications of desalination. Effective integration of solar energy generation and freshwater production can address both issues. This review article highlights recent key advances in such integration achieved in a joint-research university-national laboratory partnership under the auspices of the United States Department of Energy and parallel efforts worldwide. First, an overview of current and emerging desalination technologies and associated pretreatment, brine treatment, and valorization technologies that together can result in zero-liquid-discharge systems is presented, and their technological readiness levels are evaluated. Then, advanced modeling techniques and new software platforms that enable optimization of solar-desalination applications with the dual objective of cost and environmental impact minimization are discussed.

14 SOLAR ENERGY↗
DOE OSTI2026

Casimir interactions between two parallel graphene sheets carrying steady-state drift currents

Here, we investigate the fluctuation-induced Casimir interactions between two parallel graphene sheets carrying steady-state drift currents. The graphene properties are modeled based on the shifted Fermi disk model to capture the nonequilibrium optical response of the system. We find that the drift current introduces a repulsive correction to the perpendicular to the layers Casimir interaction, thereby reducing the overall attractive force. Although the correction is repulsive, it does not overcome the underlying attraction between the layers. It also generates a lateral force that opposes the carrier flow direction. Both contributions are studied in terms of distance and drift velocity functionalities showing pathways for Casimir force control.

Ke, Modi [University of South Florida, Tampa, FL (↗
DOE OSTI2024

A new HVdc Substation Architecture with Higher Power Transfer Capability

The power transferred through high voltage direct current transmission (HVdc) systems is increasing with increased resilience and reliability needs as well as large scale deployment of renewable energy systems. In this paper, a new HVdc substation (SS) architecture with higher power transfer capability is proposed. The HVdc converters or valve groups (VG) are connected in series and parallel fashion such that the total power rating of the SS is increased. The control challenges associated with such SS architecture are identified and appropriate control modifications are proposed. The same is verified through PSCAD based simulations.

Jaldanki, Sreenivasa↗