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DOE OSTI2024

First-Principles Simulation of Beam-Induced Processes Underlying Atomic Manipulation in Electron Microscopes

The development of experimental methods and apparatuses capable of promoting atomically precise material manipulations holds great promise for realizing the ultimate limit of feature miniaturization in materials and devices. The ability to modify materials atom by atom is anticipated to usher in new technologies in areas as diverse as separation science, medicine, and quantum information science. Historically, scanning probe-based techniques have been the most prominent approaches in this space. However, these methods are best suited for the manipulation of surface-exposed regions of materials, as the strong perturbations required for bond scission are delivered most effectively to atoms in the near-proximity to the scanning probe. In contrast, convergent electron beams with energies tuned slightly below the threshold for inducing irreversible knock-on damage have recently been employed (within scanning transmission electron microscopy) to promote atomic-scale bond rearrangements in various beam-stable solids. Currently, however, the efficiency and selectivity of beam-induced atomic manipulation processes with focused electron beams are such that long irradiation times are required to induce a desired atomic rearrangement. With a better understanding of the underlying physics dictating the outcome of a given irradiation event, methods can be devised to improve the efficiency of these techniques so that their promise can be fully realized through widespread adoption.To this end, this Account details our recent efforts to develop and apply tractable first-principles simulation approaches for studying the response of materials to electric beam-like external electric potentials applied in real space. We briefly review the concepts and capabilities in the area of atomically precise materials manipulation and review the early demonstrations of accomplishments in this area, focusing on studies using scanned convergent electron beam probes in particular. We expound upon the depth of the challenge and identify critical shortcomings of theoretical methods that have previously been employed in the simulation of beam-induced processes. We then describe the computational methods that we have generalized from the concepts and tools most commonly applied to the study of molecular photochemistry and how our adaptations of these methods can be employed to capture the relevant dynamical phenomena for beam-induced processes ranging from the initial electron scattering to the ensuing multistate reactions. Here, we contextualize these methods within the current state of the art in this area, which has historically focused primarily on the simulation of inelastic image formation in the electron microscope for the purpose of interpreting the results of quantitative electron microscopy experiments. We demonstrate that the spatial distribution of state-specific excitation rates due to the presence of an external (probe) electric charge is inhomogeneous, such that irradiation at particular locations in materials can favor specific electronic transitions (and disallow others). In addition to the potential for excited-state reaction pathways to be accessed through the initial inelastic scattering of the tightly focused electron beam from the targeted atoms, we also identify favorable conditions for the electronically nonadiabatic evolution of the highly vibrationally excited system to open complex multistate reaction pathways. Implications of the early results for understanding the mechanisms and potential routes to improved efficiency and selectivity in beam-induced reactions are discussed. We conclude with a summary of the current state of theory and modeling capabilities in this area and provide our perspective on future directions for theoretical and experimental developments that we view as crucial to advancing the use of convergent electron beams in mode-specific, atomically precise platforms for direct-write materials modifications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

CHEQUP v0.1

CHEQUP (Castro-based Hofi Expansion with QUasineutral Plasma) is a simulation code for modeling the formation of hydrodynamic optical-field-ionized (HOFI) plasma channels, which are used as waveguides in laser-plasma acceleration experiments. This includes experiments performed at LBNL's BELLA facility as well as other laser facilities across the world. CHEQUP extends the open-source Castro hydrodynamics framework with physics modules tailored for modeling HOFI plasma channels -- including multi-species ionization and three-body recombination for mixtures of hydrogen, nitrogen, helium, and argon ; a two-temperature model tracking electron and heavy-species temperatures separately ; and coupling with other codes of the BLAST ecosystem (https://blast.lbl.gov/) such as WarpX, via the openPMD standard. CHEQUP inherits from Castro the ability to run on modern GPU architectures (NVIDIA CUDA, AMD HIP) and supports adaptive mesh refinement (AMR) for efficient multi-scale resolution. Compared to existing tools, CHEQUP would be, to our knowledge, the first open-source code implementing the full HOFI channel formation physics, and the first implementation capable of running on GPUs. This enables significantly faster, large-scale parameter scans critical for the design of next-generation LPA-based accelerators and light sources.

Lehe, Remi [Lawrence Berkeley National Laboratory ↗

DOE OSTI2025

Virtual Reality for Shoot/No-Shoot Decision Training in Law Enforcement: A Literature Review and Research Agenda

Virtual reality (VR) can materially improve “shoot / no-shoot” (SNS) training by giving officers realistic, repeatable practice making high-stakes decisions under pressure. Traditional tools—live-fire ranges and video simulators—build basics, but they cannot adapt to each officer in real time or fully mirror the complexity of the field. VR closes that gap by creating immersive scenarios that are safer, more flexible, easier to scale across units, and able to capture objective performance data. SNS decisions are not just about marksmanship; they rely on perception, judgment, memory, and the ability to hold fire when a threat is uncertain. Effective training therefore needs realism, decision complexity, and branching outcomes that reflect the true consequences of choices. These elements strengthen recognition of hostile intent while reducing false positives and building the self-control required in ambiguous situations. VR brings specific advantages: dynamic environments, full-body interaction, and the ability to measure performance with precision—enabling targeted feedback and better transfer of learning to the street. At the same time, responsible deployment must address scenario quality (credible environments and behaviors), lawful decision models, and user wellbeing (appropriate stress levels, comfort, and safety). Sandia’s VIPER Lab is positioned to lead this work. The team combines human-performance science, AI/ML, and VR/AR development with a deep equipment bench (e.g., omnidirectional treadmill, eye-tracking, haptics, multiple HMDs). This ecosystem supports building and validating next-generation SNS training that is immersive, measurable, and trustworthy. Bottom line: Investment in VR-enabled SNS training that blends evidence-based design with careful validation and legal safeguards is expected to pay off in safer, more consistent decision-making and improved community trust, delivered through training that is practical to deploy at scale.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

NASA NTRS1982

Component-specific modeling

The ability to accurately structurally analyze engine components to assure that they can survive for their designed lifetime in an increasingly harsh environment is discussed. Under the HOST (HOt Section Technology) program, advanced component-specific modeling methods, with built-in analysis capability, will be developed separately for burner liners, turbine blades and vanes. These modeling methods will make maximum use of, but will not rely solely on, existing analysis methods and techniques, to analyze the three identified components. Nor will the complete structural analysis of a component necessarily be performed as a single analysis. The approach to be taken will develop complete software analysis packages with internal, component-specific, self-adaptive solution strategies. Each package will contain a set of modeling and analysis tools. The selection and order of specific methods and techniques within the set to be applied will depend on the specific-component, the current thermo-mechanical loading, and the current state of the component. All modeling and analysis decisions will be made internally based on developed decision criteria within the solution strategies; minimal user intervention will be required.

Hirschbein, M. S.↗

NASA NTRS2009

Auto-Generated Semantic Processing Services

Auto-Generated Semantic Processing (AGSP) Services is a suite of software tools for automated generation of other computer programs, denoted cross-platform semantic adapters, that support interoperability of computer-based communication systems that utilize a variety of both new and legacy communication software running in a variety of operating- system/computer-hardware combinations. AGSP has numerous potential uses in military, space-exploration, and other government applications as well as in commercial telecommunications. The cross-platform semantic adapters take advantage of common features of computer- based communication systems to enforce semantics, messaging protocols, and standards of processing of streams of binary data to ensure integrity of data and consistency of meaning among interoperating systems. The auto-generation aspect of AGSP Services reduces development time and effort by emphasizing specification and minimizing implementation: In effect, the design, building, and debugging of software for effecting conversions among complex communication protocols, custom device mappings, and unique data-manipulation algorithms is replaced with metadata specifications that map to an abstract platform-independent communications model. AGSP Services is modular and has been shown to be easily integrable into new and legacy NASA flight and ground communication systems.

Davis, Rodney↗

NASA NTRS2000

Tactile Sensing for Dexterous Robotic Hands

Robotic systems will be used as precursors to human exploration to explore the solar system and expand our knowledge of planetary surfaces. Robotic systems will also be used to build habitats and infrastructure required for human presence in space and on other planetary surfaces . Such robots will require a high level of intelligence and automation. The ability to flexibly manipulate their physical environment is one characteristic that makes humans so effective at these building and exploring tasks . The development of a generic autonomous grasp ing capability will greatly enhance the efficiency and ability of robotics to build, maintain and explore. To tele-operate a robot over vast distances of space, with long communication delays, has proven to be troublesome. Having an autonomous grasping capability that can react in real-time to disturbances or adapt to generic objects, without operator intervention, will reduce the probability of mishandled tools and samples and reduce the number of re-grasp attempts due to dropping. One aspect that separates humans from machines is a rich sensor set. We have the ability to feel objects and respond to forces and textures. The development of touch or tactile sensors for use on a robot that emulates human skin and nerves is the basis for this discussion. We will discuss the use of new piezo-electric and resistive materials that have emerged on the market with the intention of developing a touch sensitive sensor. With viable tacti le sensors we will be one step closer to developing an autonomous grasping capability.

Martin, Toby B.↗

NASA NTRS2018

Performance Evaluation of Conflict-Free Trajectory Taxiing in Airport Ramp Area Using Fast-Time Simulations

The German Aerospace Center (DLR) and the National Aeronautics and Space Administration (NASA) have been collaborating to conduct joint research addressing future surface traffic management challenges. The surface management tool from DLR, called Taxi Routing for Aircraft: Creation and Controlling (TRACC), was adapted to be integrated in NASA's fast-time simulation environment called Surface Operations Simulator and Scheduler (SOSS). The research described in this paper 1) applied TRACC to trajectory-based ramp traffic management, where TRACC generates conflict-free aircraft trajectories in a congested ramp area, 2) investigated the feasibility of the concept through the integrated TRACC-SOSS fast-time simulation, and 3) evaluated the performance of the integrated system. For this activity, TRACC was adapted for ramp operations at Charlotte Douglas International Airport, called TRACC_PB (TRACC for pushback optimization). TRACC_PB provides four-dimensional taxi trajectories with a command speed profile for each aircraft following standard taxi routes within the ramp area. In this study, departures are given the Target Movement Area entry Times (TMATs) provided by the baseline surface metering scheduler based on NASA's Spot and Runway Departure Advisor (SARDA). TRACC_PB also calculates optimal pushback times for departures, as well as the times when arrivals shall enter the ramp, the Target Movement area Exit Times (TMETs). The initial results showed that the TRACC_PB successfully generated conflict-free trajectories for the ramp area taxi operations and improved taxiing efficiency compared to the baseline results. TRACC_PB aimed to provide conflict-free taxi routes avoiding any stops while taxiing. This resulted in longer gate hold times for departures and postponed throughput values compared to the baseline simulation without trajectory optimization. Having conflict-free routes without stoppage also created shorter taxi times but required renegotiation of the given TMATs. TRACC_PB also achieved reductions in both fuel consumption and engine emissions (17% for departures and 10% for arrivals), which correlate with the ramp taxi time reduction.

trajectory-based taxi operations↗

NASA NTRS2018

Enabling Experimental Evolution: Multi-Parameter Sensor System Integration into a Culture/Stressor Biofluidics System

Experimental evolution (EE) exposes microbial communities to ecological stressors, simulating dynamics up to near-extinction events. Combined with comparative sequencing and other molecular tools, such data can inform the genetic and other biological mechanisms underlying extremophile adaptation, and other observed effects. Automating this type of experiment using biofluidics can mitigate many traditional obstacles, including delays in assay results and environment adjustment and the need for many replicates. A first-generation device for automating EE procedures, the Automated Adaptive Directed Evolution Chamber (AADEC), was developed at NASA Ames. UV-C radiation was the stressor, an LED-photodiode array measured optical density, magnetic agitation and peristaltic pump systems ensured nutrient availability, and Arduino microcontrollers provided control. Escherichia coli in LB kanamycin media was used for testing and performance verification. A manual laboratory procedure with timed exposure to UV-C was performed to typify tolerance acquisition. Approximately a 106 factor increase in survival ratio was recorded over multiple iterations. Currently, a second-generation device is being developed integrating more real-time sensors: redox potential (ORP), indicating available/consumed metabolic energy; dissolved oxygen (DO), indicating aerobic/anaerobic growth; pH, indicating metabolic products; and electrical conductivity (EC), another indicator of metabolic products. The EC sensor system was constructed and calibrated in-house and matched commercial sensors in the required range. A Raspberry Pi computer automated the electrical system, allowing real-time data acquisition. The fluidics card was made of CNC-milled polycarbonate for biocompatibility. Each sensor parameter can also be used as a selection pressure alone or in combination with others to create extreme microbial environments. As a proof of concept, this work demonstrated sensor operation in one pair of growth-sensor chambers. It can be expanded to a multi-chamber system to enable inter-culture comparisons and multi-population studies. The prior Arduino system will be ported to the RPi system. Future stressors to be added include thermal, reactive oxygen species, and varying nutrient availability.

Govinda Raj, Chinmayee↗

NASA NTRS2020

Unprecedented Drought Challenges for Texas Water Resources in a Changing Climate: What Do Researchers and Stakeholders Need to Know?

Long‐range water planning is complicated by factors that are rapidly changing in the 21st century, including climate, population, and water use. Here, we analyze climate factors and drought projections for Texas as an example of a diverse society straddling an aridity gradient to examine how the projections can best serve water stakeholder needs. We find that climate models are robust in projecting drying of summer‐season soil moisture and decreasing reservoir supplies for both the eastern and western portions of Texas during the 21st century. Further, projections indicate drier conditions during the latter half of the 21st century than even the most arid centuries of the last 1,000 years that included megadroughts. To illustrate how accounting for drought non‐stationarity may increase water resiliency, we consider generalized case studies involving four key stakeholder groups: agricultural producers, large surface water suppliers, small groundwater management districts, and regional water planning districts. We also examine an example of customized climate information being used as input to long‐range water planning. We find that while stakeholders value the quantitative capability of climate model outputs, more specific climate‐related information better supports resilience planning across multiple stakeholder groups. New suites of tools could provide necessary capacity for both short and long‐term, stakeholder‐specific adaptive planning.

drought↗

NASA NTRS2022

Feedback-Directed Random Sequence Generation for Verifying Spacecraft Flight Rule Violations

The Psyche: Journey to a Metal World mission will be launched in 2022 to study the largest metal asteroid in the main asteroid belt, (16) Psyche. The spacecraft will perform a Mars Flyby in 2023 and enter (16) Psyche’s orbit in 2026. Throughout the mission, safely operating the spacecraft will require abiding by a set of flight rules that can be defined at any point in the mission lifecycle. These flight rules ensure that the spacecraft is operating within allowed regimes and a discrete event simulation tool, SEQGEN, will be used to model all command sequences prior to uplink. One of SEQGEN’s responsibilities is to determine if a command sequence violates any flight rules. For each flight rule, the necessary logic to determine if a violation has occurred is implemented in the SEQGEN adaptation, which is maintained by the mission. This adaptation must be tested thoroughly to ensure that the flight rule logic was interpreted and implemented correctly. This work describes a tool, RandSEQ, that autogenerates a suite of flight rule violating test sequences for each flight rule implemented in SEQGEN, and can be used by any mission using SEQGEN. The Psyche SEQGEN adaptation is still being developed, but so far, RandSEQ has been used to generate 532 test cases, that can be reviewed by various stakeholders, for 40 flight rules. The ability to autogenerate these test cases has significantly reduced the amount of time required to implement and test each flight rule.

Su, Laura↗

NASA NTRS2004

Developing parallel GeoFEST(P) using the PYRAMID AMR library

The PYRAMID parallel unstructured adaptive mesh refinement (AMR) library has been coupled with the GeoFEST geophysical finite element simulation tool to support parallel active tectonics simulations. Specifically, we have demonstrated modeling of coseismic and postseismic surface displacement due to a simulated Earthquake for the Landers system of interacting faults in Southern California. The new software demonstrated a 25-times resolution improvement and a 4-times reduction in time to solution over the sequential baseline milestone case. Simulations on workstations using a few tens of thousands of stress displacement finite elements can now be expanded to multiple millions of elements with greater than 98% scaled efficiency on various parallel platforms over many hundreds of processors. Our most recent work has demonstrated that we can dynamically adapt the computational grid as stress grows on a fault. In this paper, we will describe the major issues and challenges associated with coupling these two programs to create GeoFEST(P). Performance and visualization results will also be described.

adaptive mesh refinement (AMR)↗

DOE OSTI2024

Translating macroecological models to predict microbial establishment probability in an agricultural inoculant introduction

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2015

Virtual Reality as a Medium for Sensorimotor Adaptation Training and Spaceflight Countermeasures

With the upcoming shift to extra‐long duration missions (1 year) aboard the ISS, sensorimotor adaptations during transitory periods in‐and‐out of microgravity are more important to understand and prepare for. Advances in virtual reality technology enables everyday adoption of these tools for entertainment and use in training. Experiencing virtual environments (VE) allows for the manipulation of visual flow to elicit automatic motor behavior and produce sensorimotor adaptation (SA). Recently, the ability to train individuals using repeatable and varied exposures to SA challenges has shown success by improving performance during exposure to a novel environment (Batson 2011). This capacity to 'learn to learn' is referred to as sensorimotor adaptive generalizability and, through the use of treadmill training, represents an untapped potential for individualized countermeasures. The goal of this study is to determine the feasibility of present head mounted displays (HMDs) to produce compelling visual flow information and the expected adaptations for use in future SA treadmill‐based countermeasures. Participants experience infinite hallways providing congruent (baseline) or incongruent visual information (half or double speed) via HMD while walking on an instrumented treadmill at 1.1m/s. As gait performance approaches baseline levels, an adaptation time constant is derived to establish individual time‐to‐adapt (TTA). It is hypothesized that decreasing the TTA through SA treadmill training will facilitate sensorimotor adaptation during gravitational transitions. In this way, HMD technology represents a novel platform for SA training using off‐the‐shelf consumer products for greater training flexibility in astronaut and terrestrial applications alike.

Madansingh, S.↗

NASA NTRSDate not supplied

Improved Heat Transfer Prediction for High-Speed Flows over Blunt Bodies using Adaptive Mixed-Element Unstructured Grids

Aerothermodynamic prediction is important for the design and analysis of many aerospace vehicles. Computational Fluid Dynamics (CFD) tools used for these predictions commonly rely on structured shock-aligned grids due to the strong shocks exhibited at high speeds. This work details the incorporation of an improved HLLE++ scheme for both perfect gas and thermochemical nonequilibrium flows which robustly captures shock waves on both non-shock-aligned and shock-aligned grids. The HLLE++ scheme reduces the impact of eigenvalue limiting on flow solutions which is required for Roe's scheme for high Mach number flows. An adapted grid approach is also demonstrated using mixed-element unstructured grids to improve heat prediction. Thin prismatic boundary layers are used with tetrahedra in the farfield and for capturing shock waves. Various results are presented for hypersonic flows over blunt bodies including cylinders, spheres, and capsules.

CFD↗

NASA NTRSDate not supplied

Improved Heat Transfer Prediction for High-Speed Flows over Blunt Bodies using Adaptive Mixed-Element Unstructured Grids

CFD↗

NASA NTRS2017

Adaptive Management Using Remote Sensing and Ecosystem Modeling in Response to Climate Variability and Invasive Aquatic Plants for the California Sacramento-San Joaquin Delta Water Resource

The California Sacramento-San Joaquin River Delta is the hub for California's water supply and supports important ecosystem services, agriculture, and communities in Northern to Southern California. Expansion of invasive aquatic plants in the Delta coupled with impacts of changing climate and long-term drought is detrimental to the San Francisco Bay/California Delta complex. NASA Ames Research Center and the USDA-ARS partnered with the State of California to develop science-based, adaptive-management strategies for invasive aquatic plant in the Sacramento-San Joaquin Delta. Specific mapping tools developed utilizing satellite and airborne platforms provide regular assessments of population dynamics on a landscape scale and support both strategic planning and operational decision making for resource managers. San Joaquin and Sacramento River watersheds water quality input to the Delta is modeled using the Soil-Water Assessment Tool (SWAT) and a modified SWAT tool has been customized to account for unique landscape and management of agricultural water supply and drainage within the Delta. Environmental response models for growth of invasive aquatic weeds are being parameterized and coupled with spatial distribution/biomass density mapping and water quality to study ecosystem response to climate and aquatic plant management practices. On the water validation and operational utilization of these tools by management agencies and how they are improving decision making, management effectiveness and efficiency will be discussed. The project combines science, operations, and economics related to integrated management scenarios for aquatic weeds to help land and water resource managers make science-informed decisions regarding management and outcomes.

Adaptive↗

NASA NTRS2002

Plant adaptation to low atmospheric pressures: potential molecular responses

There is an increasing realization that it may be impossible to attain Earth normal atmospheric pressures in orbital, lunar, or Martian greenhouses, simply because the construction materials do not exist to meet the extraordinary constraints imposed by balancing high engineering requirements against high lift costs. This equation essentially dictates that NASA have in place the capability to grow plants at reduced atmospheric pressure. Yet current understanding of plant growth at low pressures is limited to just a few experiments and relatively rudimentary assessments of plant vigor and growth. The tools now exist, however, to make rapid progress toward understanding the fundamental nature of plant responses and adaptations to low pressures, and to develop strategies for mitigating detrimental effects by engineering the growth conditions or by engineering the plants themselves. The genomes of rice and the model plant Arabidopsis thaliana have recently been sequenced in their entirety, and public sector and commercial DNA chips are becoming available such that thousands of genes can be assayed at once. A fundamental understanding of plant responses and adaptation to low pressures can now be approached and translated into procedures and engineering considerations to enhance plant growth at low atmospheric pressures. In anticipation of such studies, we present here the background arguments supporting these contentions, as well as informed speculation about the kinds of molecular physiological responses that might be expected of plants in low-pressure environments.

NASA Discipline Plant Biology↗