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DOE OSTI2017

Next Generation RivGen Power System: Kvichak River, AK Overwinter Ice Study

The University of Alaska Fairbanks (UAF) Alaska Hydrokinetic Energy Research Center was tasked with developing a real-time data telemetry / remote power generation system to monitor frazil ice conditions in the Kvichak River in support of the U.S. Department of Energy funded "Next Generation MHK River Power System Optimized for Performance, Durability and Survivability" project. A real-time telemetry system was requested because of the short time span between the end of the frazil ice season when the instruments would be recovered, limited vessel availability and the project end-date. To meet the project objectives, UAF designed and assembled a remote power/real-time data telemetry system that included an auto start propane generator, a small PV array, a small battery bank and line-of-sight radios as well as two sonar systems to monitor river velocity and water column acoustic backscatter strength. Both sonars included internal batteries for powering the instruments in case of failure of the shore based power system. The sonars, deployed in ~5 m of water on the bed of the Kvichak River, adjacent to the Village of Igiugig, Alaska were tethered to shore via a waterproof armored cable that conveyed power to the subsurface instruments and data from the instruments to the shore based telemetry system. The instruments were programmed to record data internally as well as to transmit data serially over the cables to the shore based system. The system was in-place between November, 2016 and June, 2017. While the real-time data telemetry system was not successful and the remote power generation power system was only partially successful, the system design included sufficient redundant power in the form of internal instrument batteries to enable the collection of nearly three months of overlapping velocity and backscatter data (from November through February) and a record of acoustic backscatter strength spanning the entire ~150 day frazil ice season between November, 2016 and ~April, 2017. This submission includes the overwinter ice study plan, raw data, and report.

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

TEAMER: Drifting Hydrophone System - Block Diagram and Pre-Amplifier Calibrations

This data release is part of TEAMER RFTS 2, where the Cooperative Institute for Marine Resources Studies (CIMRS) at Oregon State University is performing hardware and software development and integration of four newly designed drifting hydrophone systems for underwater noise measurements at marine renewable energy projects. These new acoustic systems will provide advanced technology support available for use at both tidal and wave energy deployments adding additional resources to the limited amount of drifting hydrophone technologies that are available to the marine energy community The submission data contains 2 files plus a Post-Access Report: One file containing the calibration parameters for four (4) pre-amplifier boards used on the drifting hydrophones. Pre-amplifier boards are model "WB PREAMP REV6," with serial numbers; 28, 29, 30, and 31. One image file illustrating the system functional block diagram of the drifting hydrophone system configuration.

16 TIDAL AND WAVE POWER↗

DOE OSTI2018

FACE-MDS Phase 2: Data from Six US-Located Elevated CO2 Experiments

This dataset contains measured ecosystem data from four Free Air CO2 Enrichment (FACE) experiments–Duke, Oak Ridge (ORNL), and Rhinelander -- and one Open Top Chamber (OTC) experiment -- Kennedy Space Center (KSCO). The sites were located in the United States and contain data from 1996-2009. These sites were the study sites of the FACE Model Data Synthesis (FACE-MDS) project phase 2. The file naming convention can be found in the file 'facemds-file-table-sitedata.xml' and information about variable naming convention can be found in the file 'facemds-standard-name-table-modvars.xml'. We followed the ALMA v3 convention for meteorological variables and developed a hierarchical naming scheme for ecosystem variables. Additional info can be found in the protocols in the accompanying meteorological dataset (Walker et al. 2018: doi:10.15485/1480328). We replaced the original naming convention mentioned in the protocol with the one described in 'facemds-standard-name-table-modvars.xml'. The outputs of the FACE-MDS phase 2 are in Walker et al (2018: doi:10.15485/1480327). The dataset contains 18 data files that are available in comma-separate (*.csv), and 18 R Data Serialization (*.rds) format. 2 XML (*.xml) companion files and additional metadata are provided: 2 data dictionaries and a file-level metadata file in comma-separate (.csv) format and a user guide in PDF (*.pdf) format. This dataset was updated on 2019-06-28 to fix daily files at Duke and ORNL were incorrectly labelled and were standard error files instead of plot level data. Now corrected and all three (plot, mean, standard error) daily data files for both sites have been added. This dataset was updated on 2026-06-08 to add a user guide, data dictionary file, and a file-level metadata file. DUKE_ax_v2.csv was added to match the no data value format of other files in this dataset. DUKE_ax.csv is maintained as a data file. No previously released data values were changed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Soil water content, matric potential, carbon dioxide and oxygen concentrations, Oct 2018-Dec 2021, Slate River Floodplain, Crested Butte, Colorado

This data package includes a time series of soil sensor data (temperature, water content, bulk electrical conductivity, porewater dissolved oxygen and porewater dissolved carbon dioxide) in a vertical profile from the Slate River floodplain outside Crested Butte, Colorado, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The package includes: (1) soil temperature, volumetric water content and electrical conductivity at 40, 60 and 82.5 cm depth; (2) soil matric potential at 40, 60, 79 and 100 cm depth; (3) soil CO2 concentrations at 40, 60 and 82.5 cm depth; and (4) soil oxygen concentrations at 60, 82.5, 100, 135, 170 and 182 cm depth. Both the carbon dioxide and oxygen sensors are optical sensors that can measure the partial pressure of oxygen in both saturated and unsaturated conditions. Unfortunately, soil CO2 in the profile is unexpectedly high and above the sensor calibration range (0-25,000 ppm). In addition, soil CO2 sensors failed within a year of deployment, so we only report CO2 data from 2019-2020.Within the data package, "FLMD.csv" describes file-level metadata and "dd.csv" defines column headers and universal terms across the dataset. The data package includes 4 "*data.csv" files, one for each calendar year in the dataset. Each "*data.csv" file has a corresponding "*_InstallationMethods.csv" file that describes the location, sensor model, sensor serial number and other metadata corresponding for each measured parameter. Because sensors have been added over time, not every sensor has data dating back to Oct 2018. Note that there is a data gap over winter 2019-2020 due to a power outage. While this repository currently only contains data through December 2021, the dataset will be updated as additional years are collected and processed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Meteorological, reference evapotranspiration and estimated transpiration data, July 2020-Dec 2021, Slate River Floodplain, Crested Butte, Colorado

This data package includes a time series of meteorological data (air temperature, relative humidity, barometric pressure, precipitation, wind speed, soil heat flux, incoming shortwave radiation, incoming longwave radiation, outgoing shortwave radiation and outgoing longwave radiation) from the Slate River floodplain outside Crested Butte, Colorado, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The package also includes reference evapotranspiration calculated via the Penman-Monteith equation and an estimate of willow (Salix spp.) evapotranspiration using the method of Irmak et al., J. Hydrology, 2013. Due to two malfunctioning sensors (incoming shortwave radiation from Oct 2020-May 2021 and incoming longwave radiation from May 2021-March 2022), observed net radiation and calculated evapotranspiration are only included from July-October 2020. However, users may be able to extend calculated evapotranspiration using estimates of these two parameters from other sources. Both sensors have been replaced and data beyond 2021 be uploaded to this repository when it is available.Within the data package, "FLMD.csv" describes file-level metadata and "dd.csv" defines column headers and universal terms across the dataset. The data package includes 3 "*data.csv" files, two for meteorological data for 2020 and 2021 and one for reference evapotranspiration and transpiration data from 2020 ("SLT_OBJ2_PenmanMonteith_2020_data.csv"). Each "*data.csv" file of meteorological data has a corresponding "*_InstallationMethods.csv" file that describes the location, sensor model, sensor serial number and other metadata corresponding to each measured parameter. We also include a Jupyter notebook ("PenmanMonteithET_Calculations.ipynb") that details the assumptions and equations used to calculate daily and hourly reference evapotranspiration and daily willow transpiration from raw meteorological data.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Bayesian inference of Stochastic reaction networks using Multifidelity Sequential Tempered Markov Chain Monte Carlo

Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells.These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic frame-work for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty.Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Metropolis-Hastings algorithm involve numerous serial evaluations of the likelihood function, which in turn requires expensive forward solutions of the chemical master equation (CME). We propose an alternate approach based on a multifidelity extension of the Sequential Tempered Markov Chain Monte Carlo (ST-MCMC) sampler. This algorithm is built upon Sequential Monte Carlo and solves the Bayesian inference problem by decomposing it into a sequence of efficiently solved subproblems that gradually increase both model fidelity and the influence of the observed data. We reformulate the finite state projection (FSP) algorithm, a well-known method for solving the CME, to produce a hierarchy of surrogate master equations to be used in this multifidelity scheme. To determine the appropriate fidelity, we introduce a novel information-theoretic criteria that seeks to extract the most information about the ultimate Bayesian posterior from each model in the hierarchy without inducing significant bias. This novel sampling scheme is tested with high performance computing resources using biologically relevant problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

NEW EPICS/RTEMS IOC BASED ON ALTERA SOC AT JEFFERSON LAB

A new EPICS/RTEMS IOC based on the Altera System-on-Chip (SoC) FPGA is being designed at Jefferson Lab. The Altera SoC FPGA integrates a dual ARM Cortex-A9 Hard Processor System (HPS) consisting of processor, peripherals and memory interfaces tied seamlessly with the FPGA fabric using a high-bandwidth interconnect backbone. The embedded Altera SoC IOC has features of remote network boot via U-Boot from SD card or QSPI Flash, 1Gig Ethernet, 1GB DDR3 SDRAM on HPS, UART serial ports, and ISA bus interface. RTEMS for the ARM processor BSP were built with CEXP shell, which will dynamically load the EPICS applications at runtime. U-Boot is the primary bootloader to remotely load the kernel image into local memory from a DHCP/TFTP server over Ethernet, and automatically run RTEMS and EPICS. The first design of the SoC IOC will be compatible with Jefferson Lab’s current PC104 IOCs, which have been running in CEBAF 10 years. The next design would be mounting in a chassis and connected to a daughter card via standard HSMC connectors. This standard SoC IOC will become the next generation of low-level IOC for the accelerator controls at Jefferson Lab.

Yan, Jianxun↗

DOE OSTI2025

Redesign of the Timeline Generator at Fermilab using a web-based Flutter application, GraphQL API and an IOC

The control system at Fermilab is undergoing an evolution with a shift towards web-based applications with connections to the EPICS infrastructure. The Timeline Generator (TLG) is an application that serves to coordinate events across the lab using different timing links. These links include the Tevatron clock (TCLK), a 10 MHz serial link with events encoded at 20Hz and Machine Data (MDAT), a communication link with states encoded at 720Hz. This paper covers the redesign of the major components of the TLG. This includes a web-based Flutter application for building timelines. A placement service is in use that has a GraphQL interface and uses a timeline input to compute a schedule of events and states. The Flutter application sends this computed schedule to the TLG IOC via a GraphQL interface to the Data Pool Manager (DPM). The TLG IOC runs on an Arria FPGA, the Accelerator Clock Generator (ACLK-GEN), which is responsible for writing the events and states on to the different timing links.

Carmichael, Linden [Fermilab]↗

DOE OSTI2017

Status of the LCLS-II Accelerating Cavity Production

Cavity serial production for the LCLS-II 4 GeV CM SRF linac has started. A quantity of 266 accelerating cavities has been ordered from two industrial vendors. Jefferson Laboratory leads the cavity procurement activities for the project and has successfully transferred the Nitrogen-Doping process to the industrial partners in the initial phase, which is now being applied for the production cavities. We report on the results from vendor qualification and the status of the cavity production for LCLS-II.

Daly, Ed↗

DOE OSTI2026

The Ghost Collider: An Innovative Higgs Factory

The Ghost Collider is an innovative proposal for a 550 GeV centre-of-mass, 275 GeV per beam linear collid-er with four interaction regions, each with the design luminosity. The primary innovation is the use of “ghost bunches” containing equal numbers of electrons and posi-trons so they are electrically neutral. In the linacs, energy is transferred between electrons and positrons in the same bunch, decelerating one type of particle and using the energy to accelerate the other: a new class of Energy Re-covery Linacs. At the interaction points, collisions be-tween two neutral ghost bunches occurs with weakened electromagnetic interaction such as the beam-beam effect or disruption, ensuring that the particles and their energy can be recycled with minimal loss. Four “serial IPs” are incorporated, where chromatic errors produced in one IP are cancelled in the following IP. The neutral beam insta-bility at the IP is also addressed. All interaction points have the nominal luminosity per IP of 2.8 x 1034 cm-2s-1 for a facility luminosity of 1.1 x1035 cm-2s-1 @ 100 MW electrical power for the RF systems. The result is a totally original concept for an electron-positron collider.

Hutton, A. [Thomas Jefferson National Accelerator ↗

DOE OSTI2026

Chromaticity compensation of a ghost collider

The GHOST collider final focus system is a pure quadrupole-drift beamline targeting ¿* = 2 mm at four serial interaction points, with peak ¿-functions reaching ~65 km in the final triplet. Beam tracking simulations reveal that a nominal bunch develops a pronounced C-shape in longitu- dinal phase space at IP1, with ¿¿ growing from 0.15 mm to ~2.3 mm — a factor of ~15× increase that directly re- duces luminosity. The mechanism is identified as chromat- ically amplified betatron path length: off-momentum par- ticles acquire enlarged betatron amplitudes in the high-¿ final triplet, generating excess path length via the geometric ¿¿ = - 1/2 ¿ (¿'2 + ¿'2) ¿¿ integral. Within the monoenergetic Balandin framework, ¿2¿2 with ¿ = - 1/2 ¿ ¿ ¿¿ dominates ¿2¿2 by over four million times; the full beam ¿¿ is a fur- ther factor of ~27 larger, driven by ¿¿ -induced chromatic amplitude growth. Phase-advance scans confirm that ¿¿ is insensitive to the apochromatic (¿ ˜ 0) condition. When combined with the geometric hourglass effect, this distor- tion poses a challenge to maximizing luminosity within the current lattice design.

Gamage, B. [Thomas Jefferson National Accelerator ↗

DOE OSTI2016

Prostate extracellular vesicles in patient plasma as a liquid biopsy platform for prostate cancer using nanoscale flow cytometry

Background: Extracellular vesicles released by prostate cancer present in seminal fluid, urine, and blood may represent a non-invasive means to identify and prioritize patients with intermediate risk and high risk of prostate cancer. We hypothesize that enumeration of circulating prostate microparticles (PMPs), a type of extracellular vesicle (EV), can identify patients with Gleason Score≥4+4 prostate cancer (PCa) in a manner independent of PSA. Patients and Methods: Plasmas from healthy volunteers, benign prostatic hyperplasia patients, and PCa patients with various Gleason score patterns were analyzed for PMPs. We used nanoscale flow cytometry to enumerate PMPs which were defined as submicron events (100-1000nm) immunoreactive to anti-PSMA mAb when compared to isotype control labeled samples. Levels of PMPs (counts/µL of plasma) were also compared to CellSearch CTC Subclasses in various PCa metastatic disease subtypes (treatment naïve, castration resistant prostate cancer) and in serially collected plasma sets from patients undergoing radical prostatectomy. Results: PMP levels in plasma as enumerated by nanoscale flow cytometry are effective in distinguishing PCa patients with Gleason Score≥8 disease, a highrisk prognostic factor, from patients with Gleason Score≤7 PCa, which carries an intermediate risk of PCa recurrence. PMP levels were independent of PSA and significantly decreased after surgical resection of the prostate, demonstrating its prognostic potential for clinical follow-up. CTC subclasses did not decrease after prostatectomy and were not effective in distinguishing localized PCa patients from metastatic PCa patients. Conclusions: PMP enumeration was able to identify patients with Gleason Score ≥8 PCa but not patients with Gleason Score 4+3 PCa, but offers greater confidence than CTC counts in identifying patients with metastatic prostate cancer. CTC Subclass analysis was also not effective for post-prostatectomy follow up and for distinguishing metastatic PCa and localized PCa patients. Nanoscale flow cytometry of PMPs presents an emerging biomarker platform for various stages of prostate cancer.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

The BayREN Integrated Commercial Retrofits (BRICR) Project: An Introduction and Preliminary Results

BayREN Integrated Commercial Retrofits (BRICR) is a DOE-funded project which aims to enhance the capacity of energy efficiency programs to recruit participants, develop retrofits, and measure outcomes in small and medium-sized commercial buildings, a sector notoriously hard to reach and expensive to serve, that accounts for 2/3 of US commercial floor space. To address these barriers, BRICR leverages existing incentives, financing, data, and open source software to facilitate two paths for comprehensive improvements: a deep energy retrofit, or serial upgrades integrated into capital improvement and maintenance cycles. BRICR is developing an integrated workflow for iterative energy modeling of commercial buildings for city energy program managers and auditors - starting with mass building-scale simulation based on public records and proceeding through audit, retrofit, and measurement and verification stages. BRICR builds on existing tools including LBNL’s CBES, NREL’s OpenStudio, PNNL’s Audit Template, and DOE’s BuildingSync and SEED PlatformTM. At each stage, BRICR uses available information to inform simulations (starting with public records but iteratively augmented with observations from energy program staff) to improve the quality of the models that inform decision making. This paper presents initial results from energy models of 1699 office and retail buildings in San Francisco. Building stock data from public records were translated to create a BuildingSync file for each building which was stored in SEED. Each BuildingSync file was then translated to multiple OpenStudio Workflow files for EnergyPlus simulation to estimate energy savings of energy conservation measures (ECM). Energy savings predictions for each ECM were written back to an updated BuildingSync file for each building and re-uploaded to SEED. The distribution of baseline energy simulations was calibrated against the publicly disclosed distribution of energy benchmarking data to increase confidence in results.

Piette, M↗

DOE OSTI2022

Cabana: A Performance Portable Library for Particle-Based Simulations

Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

MontePy: a Python library for reading, editing, and writing MCNP input files.

The Monte Carlo N-Particle (MCNP) radiation transport code is a highly capable and accurate code with a long legacy. MCNP uses the Monte Carlo simulation process to simulate the path of particles (e.g., neutrons, photons, charged particles, etc.), and their interaction with materials. It is widely used in nuclear engineering, high-energy physics, and other fields. Its origins in the mid-twentieth century predate many modern software conventions. MCNP users provide an input file to MCNP, which it then uses to create an internal representation of the simulation problem. These input files originally had to be stored as punchcard decks, and the user manual still uses the terminology of cards and decks, despite moving beyond punchcards. MCNP predates nearly all modern human readable markup or data serialization languages, such as the extensible Markup Language (XML), the Standard Generalized Markup Language (SGML), YAML (YAML Ain’t Markup Language), and Javascript Object Notation (JSON). Due to this, MCNP uses an entirely custom defined syntax language for its input, making off-the-shelf libraries for XML, YAML, and JSON impossible to use for scripting various operations on MCNP input files (Kulesza et al., 2022).

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Reduce, reuse, reinterpret: An end-to-end pipeline for recycling particle physics results

Searches for new physics at the Large Hadron Collider have constrained many models of physics beyond the Standard Model. Many searches also provide resources that allow them to be reinterpreted in the context of other models. We describe a reinterpretation pipeline that examines previously untested models of new physics using supplementary information from ATLAS Supersymmetry (SUSY) searches in a way that provides accurate constraints even for models that differ meaningfully from the benchmark models of the original analysis. The public analysis information, such as public analysis routines and serialized probability models, is combined with common event generation and simulation toolkits MADGRAPH, PYTHIA8, and DELPHES into workflows steered by TOML configuration files, and bundled into the mapyde Python package. The use of mapyde is demonstrated by constraining previously untested SUSY models with compressed sleptons and electroweakinos using ATLAS results.

Stark, Giordon↗

DOE OSTI2024

Codebase release 0.5 for mapyde

Stark, Giordon↗

DOE OSTI2013

Templated Self Assemble of Nano-Structures

This project will identify and model mechanisms that template the self-assembly of nanostructures. We focus on a class of systems involving a two-phase monolayer of molecules adsorbed on a solid surface. At a suitably elevated temperature, the molecules diffuse on the surface to reduce the combined free energy of mixing, phase boundary, elastic field, and electrostatic field. With no template, the phases may form a pattern of stripes or disks. The feature size is on the order of 1-100 nm, selected to compromise the phase boundary energy and the long-range elastic or electrostatic interaction. Both experimental observations and our theoretical simulations have shown that the pattern resembles a periodic lattice, but has abundant imperfections. To form a perfect periodic pattern, or a designed aperiodic pattern, one must introduce a template to guide the assembly. For example, a coarse-scale pattern, lithographically defined on the substrate, will guide the assembly of the nanoscale pattern. As another example, if the molecules on the substrate surface carry strong electric dipoles, a charged object, placed in the space above the monolayer, will guide the assembly of the molecular dipoles. In particular, the charged object can be a mask with a designed nanoscale topographic pattern. A serial process (e.g., e-beam lithography) is necessary to make the mask, but the pattern transfer to the molecules on the substrate is a parallel process. The technique is potentially a high throughput, low cost process to pattern a monolayer. The monolayer pattern itself may serve as a template to fabricate a functional structure. This project will model fundamental aspects of these processes, including thermodynamics and kinetics of self-assembly, templated self-assembly, and self-assembly on unconventional substrates. It is envisioned that the theory will not only explain the available experimental observations, but also motivate new experiments.

77 NANOSCIENCE AND NANOTECHNOLOGY↗