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DOE OSTI2016

Computational approaches to substrate-based cell motility

Substrate-based crawling motility of eukaryotic cells is essential for many biological functions, both in developing and mature organisms. Motility dysfunctions are involved in several life-threatening pathologies such as cancer and metastasis. Motile cells are also a natural realization of active, self-propelled ‘particles’, a popular research topic in nonequilibrium physics. Finally, from the materials perspective, assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography, elasticity, and surface chemistry of the environment and react to external stimuli. Although a comprehensive understanding of substrate-based cell motility remains elusive, progress has been achieved recently in its modeling on the whole cell level. Furthermore we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organized systems such as living cells.

25 ENERGY STORAGE↗

DOE OSTI2022

Post-Marcus Theory and Simulation of Interfacial Charge Transfer Dynamics in Organic Semiconducting Materials (Final Report)

The research program developed, validated and applies predictive computational protocols for calculating charge transfer (CT) rates in complex molecular systems, including molecular dyads and triads in liquid solution and solid-state organic semiconducting (OSC) materials. We have established a transformative computational scheme that goes beyond widely used simplifications, to achieve realistic descriptions of CT processes. The approach properly addresses the contribution of molecular environment at ambient conditions to CT processes. Our approach achieves unique insight on investigated CT processes in relevant experimental efforts. The collaborative team included three principal investigators (PIs), with complimentary expertise in classical molecular dynamics simulations and data science (Cheung), state-of-the-art electronic structure calculations (Dunietz), and cutting-edge theory and simulation techniques for modeling energy, charge and coherence transfer dynamics in molecular systems (Geva).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

An on-chip phased array for non-classical light

Abstract Quantum science and technology can offer fundamental enhancements in sensing, communications and computing. The expansion from wired to wireless links is an exciting prospect for quantum technologies. For classical technologies, the advent of phased arrays enabled directional and adaptive wireless links by manipulating electromagnetic waves over free space. Here we demonstrate a phased array system on a chip that can receive, image and manipulate non-classical light over free space. We use an integrated photonic-electronic system with more than 1000 functional components on-chip to detect squeezed light. By integrating an array of 32 sub-wavelength engineered metamaterial antennas, we demonstrate a direct free-space-to-chip interface for reconfigurable quantum links. On the same chip, we implement a large-scale array of quantum-limited coherent receivers that can resolve non-classical signals simultaneously across 32 channels. With coherent readout and manipulation of these signals, we demonstrate 32-pixel imaging and spatially configurable reception of squeezed light over free space. Our work advances wireless quantum technologies that could enable practical applications in quantum communications and sensing.

Science & Technology - Other Topics↗

DOE OSTI2019

Earth System Grid Federation (ESGF) Compute Challenge

This Open Geospatial Consortium (OGC) Engineering Report (ER) describes the advancement of an Execution Management System (EMS) to support Web Processing Service (WPS) climate processes deployed on the Earth System Grid Federation (ESGF). The report introduces climate data, processes and applications into Common Workflow Language (CWL) workflows with the intent of advancing: application packaging, deployment and execution in clouds; interoperability of services in federated cyberinfrastructures; and geospatial workflows towards standardization. Work presented in this report is a direct continuation of the Earth Observation & Clouds (EOC) thread of Testbed-14. This report is expected to be of relevance to Testbed-15, both to the Earth Observation Process and Application Discovery (EOPAD) task and the Machine Learning task. This engineering report will describe: relevant work conducted in OGC Testbed-14; ESGF and its compute challenge; adaptations of existing climate processes into workflows; interoperability experiments with ESGF endpoints conforming to a common API.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Author Correction: A genomic catalog of Earth’s microbiomes

In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

How the flow affects the phase behaviour and microstructure of polymer nanocomposites

We address the issue of flow effects on the phase behaviour of polymer nanocomposite melts by making use of a recently reported Hamiltonian set of evolution equations developed on principles of non-equilibrium thermodynamics. To this end, we calculate the spinodal curve, by computing values for the nanoparticle radius as a function of the polymer radius-of-gyration for which the second derivative of the generalized free energy of the system becomes zero. Under equilibrium conditions, we recover the phase diagram predicted by Mackay et al. [Science 311, 1740 (2006)]. Under non-equilibrium conditions, we account for the extra terms in the free energy due to changes in the conformations of polymer chains by the shear flow. Overall, our model predicts that flow enhances miscibility, since the corresponding miscibility window opens up for non-zero shear rate values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation

The high-affinity receptor for IgE expressed on the surface of mast cells and basophils interacts with antigens, via bound IgE antibody, and triggers secretion of inflammatory mediators that contribute to allergic reactions. To understand how past inputs (memory) influence future inflammatory responses in mast cells, a microfluidic device was used to precisely control exposure of cells to alternating stimulatory and non-stimulatory inputs. We determined that the response to subsequent stimulation depends on the interval of signaling quiescence. For shorter intervals of signaling quiescence, the second response is blunted relative to the first response, whereas longer intervals of quiescence induce an enhanced second response. Through an iterative process of computational modeling and experimental tests, we found that these memory-like phenomena arise from a confluence of rapid, short-lived positive signals driven by the protein tyrosine kinase Syk; slow, long-lived negative signals driven by the lipid phosphatase Ship1; and slower degradation of Ship1 co-factors. This work advances our understanding of mast cell signaling and represents a generalizable approach for investigating the dynamics of signaling systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Evaluation of multiple reduced-order models to enhance confidence in global sensitivity analyses

Variance-based global sensitivity analysis (e.g., the Sobol' sensitivity index) can be used to identify the important parameters over the entire parameter space. However, one often cannot afford the computational costs of sampling-based approaches in combination with expensive high-fidelity forward models. Reduced-order models (ROM) can substantially accelerate calculation of these sensitivities. However, it is usually difficult to determine what type of ROM should be used and how accurately the ROM represents the high-fidelity model (HFM) results. Here in this paper, we propose to concurrently use multiple ROMs as a way to assess the robustness of the model-reduction method. Two sets of HFM simulations are needed, one set for building ROMs and the other for validating ROMs. Our goal is to keep the total number of HFM simulations to a minimum. Ideally some of the HFM simulations in the first set can be shared by different ROMs. Based on validation results, the ROMs can be combined with different schemes. We demonstrate that we can achieve the goal by using four different ROMs and still considerably save computational time compared to using traditional HFM simulation for calculating sensitivity indices. We apply the approach to an example problem of a large-scale geological carbon dioxide storage system, in which the objective is to calculate a sensitivity index to identify important parameters. For this problem, the locally best ROM provides better estimates than the weighted average from all ROMs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Microstructural characterization of random packings of cubic particles

Understanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders. In addition, packing of cubic salt crystals arise in various problems involving preservation of pavements, paintings, and historical monuments, mineral-fluid interactions, CO 2 sequestration in rock, and intrusion of groundwater aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We have developed a version of the random sequential addition algorithm to generate such packings, and have computed a variety of microstructural descriptors, including the radial distribution function, two-point probability function, orientational correlation function, specific surface, and mean chord length, and have studied the effect of finite system size and porosity on such characteristics. Here, the results indicate the existence of both spatial and orientational long-range order in the packing, which is more distinctive for higher packing densities.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Resilience: Concepts from Engineering, Ecology, and the Social Sciences

“Resilience” is fast becoming a key word for describing the desired result of the activities we group under the heading of “homeland security.” Department of Homeland Security (DHS) Secretary Napolitano has made resilience a key theme in her speeches, highlighting the efforts of DHS to “strengthen the resilience of ... infrastructure, computer networks, and of ... communities and citizens.” She has talked about resilience as “strengthening the ability for our systems, our cities, our towns, and our country to bounce back quickly from an attack or a natural disaster, and to be even stronger than before. This paper first provides an overview of resilience concepts from U.S. government and academic research sources. It then discusses resilience concepts and metrics from the academic literature in more detail, focusing on three types of resilience: engineering resilience, ecological resilience, and community and regional resilience. Next, it discusses system characteristics that have been associated with increased resilience. Based on this background, we propose a model of the infrastructure resilience analysis process. We then review LANL capabilities for each process element and indicate areas where capability development opportunities exist. Appendices provide additional information on funding sources and key players in infrastructure resilience, and a more detailed technical explanation of ecological resilience.

42 ENGINEERING↗

DOE OSTI2019

Downfolding of many-body Hamiltonians using active-space models: Extension of the sub-system embedding sub-algebras approach to unitary coupled cluster formalisms

Here, we discuss the extension of the recently introduced subsystem embedding subalgebra coupled cluster (SES-CC) formalism to unitary CC formalisms. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induced complete active space (CAS) effective Hamiltonian. In contrast to the standard single-reference SES-CC theory, the unitary CC approach results in a Hermitian form of the effective Hamiltonian. Additionally, for the double unitary CC (DUCC) formalism, the corresponding CAS eigenvalue problem provides a rigorous separation of external cluster amplitudes that describe dynamical correlation effects—used to define the effective Hamiltonian—from those corresponding to the internal (inside the active space) excitations that define the components of eigenvectors associated with the energy of the entire system. The proposed formalism can be viewed as an efficient way of downfolding many-electron Hamiltonian to the low-energy model represented by a particular choice of CAS. In principle, this technique can be extended to any type of CAS representing an arbitrary energy window of a quantum system. The Hermitian character of low-dimensional effective Hamiltonians makes them an ideal target for several types of full configuration interaction type eigensolvers. As an example, we also discuss the algebraic form of the perturbative expansions of the effective DUCC Hamiltonians corresponding to composite unitary CC theories and discuss possible algorithms for hybrid classical and quantum computing. Given growing interest in quantum computing, we provide energies for H 2 and Be systems obtained with the quantum phase estimator algorithm available in the Quantum Development Kit for the approximate DUCC Hamiltonians.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

SU-E-I-94: Automated Image Quality Assessment of Radiographic Systems Using An Anthropomorphic Phantom

Purpose: In a large, academic medical center, consistent radiographic imaging performance is difficult to routinely monitor and maintain, especially for a fleet consisting of multiple vendors, models, software versions, and numerous imaging protocols. Thus, an automated image quality control methodology has been implemented using routine image quality assessment with a physical, stylized anthropomorphic chest phantom. Methods: The “Duke” Phantom (Digital Phantom 07-646, Supertech, Elkhart, IN) was imaged twice on each of 13 radiographic units from a variety of vendors at 13 primary care clinics. The first acquisition used the clinical PA chest protocol to acquire the post-processed “FOR PRESENTATION” image. The second image was acquired without an antiscatter grid followed by collection of the “FOR PROCESSING” image. Manual CNR measurements were made from the largest and thickest contrast-detail inserts in the lung, heart, and abdominal regions of the phantom in each image. An automated image registration algorithm was used to estimate the CNR of the same insert using similar ROIs. Automated measurements were then compared to the manual measurements. Results: Automatic and manual CNR measurements obtained from “FOR PRESENTATION” images had average percent differences of 0.42%±5.18%, −3.44%±4.85%, and 1.04%±3.15% in the lung, heart, and abdominal regions, respectively; measurements obtained from “FOR PROCESSING” images had average percent differences of -0.63%±6.66%, −0.97%±3.92%, and −0.53%±4.18%, respectively. The maximum absolute difference in CNR was 15.78%, 10.89%, and 8.73% in the respective regions. In addition to CNR assessment of the largest and thickest contrast-detail inserts, the automated method also provided CNR estimates for all 75 contrast-detail inserts in each phantom image. Conclusion: Automated analysis of a radiographic phantom has been shown to be a fast, robust, and objective means for assessing radiographic image quality. The method reduces the burden of manual measurements and provides a means by which to monitor and compare radiographic system performance.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

SU-E-T-65: Characterization of a 2D Array for QA and Pretreatment Plan Verification

Purpose: The OCTAVIUS detector729 is a 2D array of 729 air vented cubic plane parallel ion chambers used for pretreatment verification and QA. In this study we investigated dosimetric characteristics of this system for clinical photon beam dosimetry. Methods: Detector performance evaluation included determination of the location of the effective point of measurement (EPM), sensitivity, linearity, and reproducibility of detector response, as well as output factor, dose rate, and source to surface distance (SSD) dependence. Finally, assessment of wedge modulated fields was carried out. All the evaluations were performed five times for low and high photon energies. For reference measurements, a 0.6 cc ionization chamber was used. Data analysis and comparison of the OCTAVIUS detector with reference ion chamber data was performed using the VeriSoft patient plan verification software. Results: The reproducibility and stability of the measurements are excellent, the detector showed same signal with a maximum deviation of less than 0.5% in short and long term. Results of sensitivity test showed same signal with a maximum deviation of approximately 0.1%. As the detector 729 response is linear with dose and dose rate, it can be used for the measurement at regions of high dose gradient effectively. The detector agrees with the ionization chamber measurement to within 1% for SSD range of 75 to 125 cm. Also, its measured wedge modulated profiles matched very well with ion chamber dose profiles acquired in a water tank. Conclusions: As the response of the detector 729 is linear with dose and dose rate, it can be used for the measurements in the areas of dose gradients effectively. Based on the measurements and comparisons performed, this system is a reliable and accurate dosimeter for QA and pretreatment plan verification in radiotherapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

SU-E-T-148: Efficient Verification Method for Modulated Electron Radiotherapy Treatment Plans

Purpose: For shallow tumors, modulated electron radiotherapy (MERT) promises a reduction of dose to distal organs at risk. At our institution a framework was developed in order to create treatment plans for MERT employing both forward and inverse optimization. In this work, an efficient quality assurance (QA) process is established. Methods: Treatment plans for three different tumor sites were created using an inverse optimization. These plans consist of 6–12 segments and energies between 6 and 18 MeV. An already established QA process for photon IMRT plans is now extended to additionally handle MERT plans. First, the dose distributions are calculated in a homogenous water phantom. For this task a dedicated Monte Carlo (MC) framework for MERT is used. Second, the segments are applied on a stand-alone amorphous silicon electronic portal imaging device (EPID) using a source-to-surface distance of 70 cm. This device was calibrated for electron beams in a previous work. An in-house developed analysis software, is then utilized for comparisons and evaluation of the measured and calculated dose distributions. Results: For all three plans the calculated dose distributions agree well with the measured ones. Using a 2D gamma comparison (2% of dose max/2 mm and 10% dose threshold) passing rates >98% are achieved.The dose calculation for each plan on the water phantom, using voxels of 0.2×0.2×0.2 cm{sup 3}, takes at maximum 30 min on a single core Pentium 2.66 GHz system with 6 GB RAM, to reach a statistical uncertainty of 2% (1 std. dev.). Conclusion: An already established QA procedure for IMRT photon plans was applied for MERT. The dedicated MC framework and the use of EPID measurements allow an efficient QA procedure in a clinical environment. This work was supported by Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

SU-E-T-248: Near Real-Time Analysis of Radiation Delivery and Imaging, Accuracy to Ensure Patient Safety

Purpose: To develop and optimize an effective software method for comparing planned to delivered control point machine parameters for all VARIAN TrueBeam treatments so as to permit (1) assessment of a large patient pool throughout their treatment course to quantify treatment technique specific systematic and random uncertainty of observables, (2) quantify the site specific daily imaging shifts required for target alignment, and (3) define tolerance levels for mechanical parameters and imaging parameters based on statistical analysis data gathered, and the dosimetric impact of variations. Methods: Treatment and imaging log files were directly compared to plan parameters for Eclipse and Pinnacle planned treatments via 3D, IMRT, control point, RapidArc, and electrons. Each control point from all beams/arcs (7984) for all fractions (1940) of all patients treated over six months were analyzed. At each control point gantry angle, collimator angle, couch angle, jaw positions, MLC positions, MU were compared. Additionally per-treatment isocenter shifts were calculated. Results were analyzed as a whole in treatment type subsets: IMRT, 3D, RapidArc; and in treatment site subsets: brain, chest/mediastinum, esophagus, H and N, lung, pelvis, prostate. Results: Daily imaging isocenter shifts from initial external tattoo alignment were dependent on the treatment site with < 0.5 cm translational shifts for H and N, Brain, and lung SBRT, while pelvis, esophagus shifts were ∼1 cm. Mechanical delivery parameters were within tolerance levels for all sub-beams. The largest variations were for RapidArc plans: gantry angle 0.11±0.12,collimator angle 0.00±0.00, jaw positions 0.48±0.26, MLC leaf positions 0.66±0.08, MU 0.14±0.34. Conclusion: Per-control point validation reveals deviations between planned and delivered parameters. If used in a near real-time error checking system, patient safety can be improved by equipping the treatment delivery system with additional forcing functions which by-pass human error avenues.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-F-I-27: Measurement of SAR and Temperature Elevation During MRI Scans

Purpose: The poor reliability and repeatability of the manufacturer-reported SAR values on clinical MRI systems have been acknowledged. The purpose of this study is to not only measure SAR values, but also RF-induced temperature elevation at 1.5 and 3T MRI systems. Methods: SAR measurement experiment was performed at 1.5 and 3T. Three MRI RF sequences (T1w TSE, T1w inversion recovery, and T2w TSE) with imaging parameters were selected. A hydroxyl-ethylcelluose (HEC) gelled saline phantom mimicking human body tissue was made. Human torso phantom were constructed, based on Korean adult standard anthropometric reference data (Fig.1). FDTD method was utilized to calculate the SAR distribution using Sim4Life software. Based on the results of the simulation, 4 electrical field (E-field) sensors were located inside the phantom. 55 Fiber Bragg Grating (FBG) temperature sensors (27 sensors in upper and lower cover lids, and one sensor located in the center as a reference) were located inside the phantom to measure temperature change during MRI scan (Fig.2). Results: Simulation shows that SAR value is 0.4 W/kg in the periphery and 0.001 W/kg in the center (Fig.2). One 1.5T and one of two 3T MRI systems represent that the measured SAR values were lower than MRI scanner-reported SAR values. However, the other 3T MRI scanner shows that the averaged SAR values measured by probe 2, 3, and 4 are 6.83, 7.59, and 6.01 W/kg, compared to MRI scanner-reported whole body SAR value (<1.5 W/kg) for T2w TSE (Table 1). The temperature elevation measured by FBG sensors is 5.2°C in the lateral shoulder, 5.1°C in the underarm, 4.7°C in the anterior axilla, 4.8°C in the posterior axilla, and 4.8°C in the lateral waist for T2w TSE (Fig.3). Conclusion: It is essential to assess the safety of MRI system for patient by measuring accurate SAR deposited in the body during clinical MRI.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Can Applications Recover from fsync Failures?

We analyze how file systems and modern data-intensive applications react to fsync failures. First, we characterize how three Linux file systems (ext4, XFS, Btrfs) behave in the presence of failures. We find commonalities across file systems (pages are always marked clean, certain block writes always lead to unavailability) as well as differences (page content and failure reporting is varied). Next, we study how five widely used applications (PostgreSQL, LMDB, LevelDB, SQLite, Redis) handle fsync failures. Our findings show that although applications use many failure-handling strategies, none are sufficient: fsync failures can cause catastrophic outcomes such as data loss and corruption. Our findings have strong implications for the design of file systems and applications that intend to provide strong durability guarantees.

Computer Science↗

DOE OSTI2025

Seeing is Believing: Autonomous Microscopy and the Data Revolution in Materials Science [Slides]

Machine intelligence has the potential to revolutionize materials science, enabling autonomous synthesis, self-driving characterization, and accelerated modeling. However, despite the promise, successful implementation of these methods in day-to-day research remains a challenge. This talk will delve into the reasons behind this, exploring how truly intelligent experiments are hindered by opaque experiment control, a lack of domain-specific models, and human-centric design. Through a focus on the characterization of next-generation microelectronics and energy storage materials, I will share insights from both successful and failed attempts to implement machine intelligence. We will then explore the next steps necessary to unlock the full potential of machine intelligence in materials science, creating a future where intelligent systems work seamlessly alongside researchers to drive innovation and discovery.

36 MATERIALS SCIENCE↗