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At least 1,045 records · Page 58

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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↗

DOE OSTI2013

Validation and Verification of the Correct Operation of the Spectro RS23 UV-VIS Spectrometer used in ANC122 and NF-ANC122

In September of 2011, the old qualified Bausch and Laum Spec 100 UV-Vis instrument used in the ANC122 and NF-ANC122 procedures failed its monthly calibration check. Attempts to get the system to pass by cleaning flow cells, replacing the light bulb and realigning the light path failed to get sustained reproducible results from the system. In October the decision to take it out of service was made as the system was 40+ years in age. To replace the system, a previously purchased Labomed Inc.’s spectrometer (model Spectro 23RS; Serial #: 23RS-004253) was retrieved from storage. This report shows that the Labomed Inc. system is performing as required and meeting all QC requirements listed in ANC122 and NF-ANC122. Upon submitting this report to records, the system will be considered qualified to report results to customers of C-AAC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2013

Compiling MPI for Many-Core Systems

Processors with multiple (or many) cores and shared memory are becoming ubiquitous across the com puting spectrum. MPI, the current de facto program ming model for scalable parallel applications, enforces copies between source and target processes and thus can not fully utilize shared memory and cache architectures of modern machines. To enable MPI-based programs to more fully exploit features of multi- and many-core architectures, we present a compiler-based transformation that transforms MPI processes into threads and fuses message serialization and deserialization loops such that send and receive calls can be replaced by direct memory accesses. Our compiler replaces most of the MPI communication functions with direct load/store accesses and our runtime provides a threaded MPI implementation to handle the remaining functions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Supporting 64-bit global indices in Epetra and other Trilinos packages :

The Trilinos Project is an effort to facilitate the design, development, integration and ongoing support of mathematical software libraries within an object-oriented framework. It is intended for large-scale, complex multiphysics engineering and scientific applications [2, 4, 3]. Epetra is one of its basic packages. It provides serial and parallel linear algebra capabilities. Before Trilinos version 11.0, released in 2012, Epetra used the C++ int data-type for storing global and local indices for degrees of freedom (DOFs). Since int is typically 32-bit, this limited the largest problem size to be smaller than approximately two billion DOFs. This was true even if a distributed memory machine could handle larger problems. We have added optional support for C++ long long data-type, which is at least 64-bit wide, for global indices. To save memory, maintain the speed of memory-bound operations, and reduce further changes to the code, the local indices are still 32-bit. We document the changes required to achieve this feature and how the new functionality can be used. We also report on the lessons learned in modifying a mature and popular package from various perspectives design goals, backward compatibility, engineering decisions, C++ language features, effects on existing users and other packages, and build integration.

Jhurani, Chetan↗

DOE OSTI2013

Parallel auto-correlative statistics with VTK.

This report summarizes existing statistical engines in VTK and presents both the serial and parallel auto-correlative statistics engines. It is a sequel to [PT08, BPRT09b, PT09, BPT09, PT10] which studied the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k-means, and order statistics engines. The ease of use of the new parallel auto-correlative statistics engine is illustrated by the means of C++ code snippets and algorithm verification is provided. This report justifies the design of the statistics engines with parallel scalability in mind, and provides scalability and speed-up analysis results for the autocorrelative statistics engine.

Pebay, Philippe Pierre↗

DOE OSTI2013

3013 DE Inner Container Closure Weld Corrosion Evaluation

Destructive evaluation (DE) of 3013 containers is one part of the U. S. Department of Energy Integrated Surveillance Program. During standard DE of 3013 containers, visual examinations for pitting and stress corrosion cracking (SCC) are performed on the accessible surfaces of the outer, inner, and convenience containers, which make up the 3013 container. As a result of 3013 DE additional analysis, the area near the inner container closure weld has been identified as being a region of increased corrosion susceptibility, which may provide a pathway for corrosive gases to the outer container. This area has a higher residual stress, an altered microstructure, and less corrosion resistant weld oxides as a result of the welding process as well as a lower temperature than other areas of the container, which may increase the absorption of moisture on the surface. The deposition of moisture in this stressed region could lead to pitting and stress corrosion cracking. During FY2013, the inner container closure weld area was more closely evaluated on several archived samples from DE containers. These containers included FY09 DE2, FY12 DE4, FY12 DE6 and FY12 DE7 and the Hanford High Moisture Container. The additional examinations included visual observations with a stereomicroscope, scanning electron microscopy along with energy dispersive spectroscopy for chemical analysis, and serial metallography of the sidewall and lid that are part of the inner container closure weld region. Pitting was observed in all the samples taken from the closure weld regions of the examined inner containers. This pitting was generally less 20 µm with most less than 5µm. These pits were similar in depth to those observed in the vapor exposed surfaces of teardrops in the shelf life corrosion testing. Cracking was not observed on either the vapor-exposed surfaces of the teardrop coupons or the inner container closure weld region. Further testing is necessary to determine if the conditions in the welded inner container could support SCC during the 50 year life time for the 3013 container.

36 MATERIALS SCIENCE↗