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DOE OSTI2025

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗

DOE OSTI2022

Can Common Pool Resource Theory Catalyze Stakeholder-Driven Solutions to the Freshwater Salinization Syndrome?

Freshwater salinity is rising across many regions of the United States as well as globally, a phenomenon called the freshwater salinization syndrome (FSS). The FSS mobilizes organic carbon, nutrients, heavy metals, and other contaminants sequestered in soils and freshwater sediments, alters the structures and functions of soils, streams, and riparian ecosystems, threatens drinking water supplies, and undermines progress toward many of the United Nations Sustainable Development Goals. There is an urgent need to leverage the current understanding of salinization’s causes and consequences–in partnership with engineers, social scientists, policymakers, and other stakeholders–into locally tailored approaches for balancing our nation’s salt budget. In this feature, we propose that the FSS can be understood as a common pool resource problem and explore Nobel Laureate Elinor Ostrom’s social-ecological systems framework as an approach for identifying the conditions under which local actors may work collectively to manage the FSS in the absence of top-down regulatory controls. We adopt as a case study rising sodium concentrations in the Occoquan Reservoir, a critical water supply for up to one million residents in Northern Virginia (USA), to illustrate emerging impacts, underlying causes, possible solutions, and critical research needs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

QC-GN 2 oMS 2 : a Graph Neural Net for High Resolution Mass Spectra Prediction

Predicting the mass spectrum of a molecular ion is often accomplished via three generalized approaches: rules-based methods for bond breaking, deep learning, or quantum chemical (QC) modeling. Rules-based approaches are often limited by the conditions for different chemical subspaces and perform poorly under chemical regimes with few defined rules. QC modeling is theoretically robust but requires significant amounts of computational time to produce a spectrum for a given target. Among deep learning techniques, graph neural networks (GNNs) have performed better than previous work with fingerprint-based neural networks in mass spectra prediction. To explore this technique further, we investigate the effects of including quantum chemically derived information as edge features in the GNN to increase predictive accuracy. The models we investigated include categorical bond order, bond force constants derived from extended tight-binding (xTB) quantum chemistry, and acyclic bond dissociation energies. Throughout this work, we evaluated these models against a control GNN with no edge features in the input graphs. Bond dissociation enthalpies yielded the best improvement with a cosine similarity score of 0.462 relative to the baseline model (0.437). In this work we also apply dynamic graph attention which improves performance on benchmark problems and supports the inclusion of edge features. Between implementations, we investigate the nature of the molecular embedding for spectra prediction and discuss the recognition of fragment topographies in distinct chemistries for further development in tandem mass spectrometry prediction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly

Pseudomonas alloputida KT2440 (formerly P. putida) has become both a well-known chassis organism for synthetic biology and a model organism for rhizosphere colonization. Here, we describe a CRISPR interference (CRISPRi) system in KT2440 for exploring microbe–microbe interactions in the rhizosphere and for use in industrial systems. Our CRISPRi system features three different promoter systems (XylS/P m , LacI/P lac , and AraC/P BAD ) and a dCas9 codon-optimized for Pseudomonads, all located on a mini-Tn7-based transposon that inserts into a neutral site in the genome. It also includes a suite of pSEVA-derived sgRNA expression vectors, where the expression is driven by synthetic promoters varying in strength. We compare the three promoter systems in terms of how well they can precisely modulate gene expression, and we discuss the impact of environmental factors, such as media choice, on the success of CRISPRi. We demonstrate that CRISPRi is functional in bacteria colonizing the rhizosphere, with repression of essential genes leading to a 10–100-fold reduction in P. alloputida cells per root. Finally, we show that CRISPRi can be used to modulate microbe–microbe interactions. When the gene pvdH is repressed and P. alloputida is unable to produce pyoverdine, it loses its ability to inhibit other microbes in vitro. Furthermore, our design is amendable for future CRISPRi-seq studies and in multispecies microbial communities, with the different promoter systems providing a means to control the level of gene expression in many different environments.

Bacteria↗

DOE OSTI2022

The role of pre-existing heterogeneities in materials under shock and spall

There has been a challenge for many decades to understand how heterogeneities influence the behavior of materials under shock loading, eventually leading to spall formation and failure. Experimental, analytical, and computational techniques have matured to the point where systematic studies of materials with complex microstructures under shock loading and the associated failure mechanisms are feasible. This is enabled by more accurate diagnostics as well as characterization methods. As interest in complex materials grows, understanding and predicting the role of heterogeneities in determining the dynamic behavior becomes crucial. Early computational studies, hydrocodes, in particular, historically preclude any irregularities in the form of defects and impurities in the material microstructure for the sake of simplification and to retain the hydrodynamic conservation equations. Contemporary computational methods, notably molecular dynamics simulations, can overcome this limitation by incorporating inhomogeneities albeit at a much lower length and time scale. This review discusses literature that has focused on investigating the role of various imperfections in the shock and spall behavior, emphasizing mainly heterogeneities such as second-phase particles, inclusions, and voids under both shock compression and release. Pre-existing defects are found in most engineering materials, ranging from thermodynamically necessary vacancies, to interstitial and dislocation, to microstructural features such as inclusions, second phase particles, voids, grain boundaries, and triple junctions. This literature review explores the interaction of these heterogeneities under shock loading during compression and release. Systematic characterization of material heterogeneities before and after shock loading, along with direct measurements of Hugoniot elastic limit and spall strength, allows for more generalized theories to be formulated. Further, continuous improvement toward time-resolved, in situ experimental data strengthens the ability to elucidate upon results gathered from simulations and analytical models, thus improving the overall ability to understand and predict how materials behave under dynamic loading.

36 MATERIALS SCIENCE↗

DOE OSTI2023

A Predictor-Corrector Strategy for Adaptivity in Dynamical Low-Rank Approximations

Here, in this paper, we present a predictor-corrector strategy for constructing rank-adaptive, dynamical low-rank approximations (DLRAs) of matrix-valued ODE systems. The strategy is a compromise between (i) low-rank step-truncation approaches that alternately evolve and compress solutions and (ii) strict DLRA approaches that augment the low-rank manifold using subspaces generated locally in time by the DLRA integrator. The strategy is based on an analysis of the error between a forward temporal update into the ambient full-rank space, which is typically computed in a step-truncation approach before recompressing, and the standard DLRA update, which is forced to live in a low-rank manifold. We use this error, without requiring its full-rank representation, to correct the DLRA solution. A key ingredient for maintaining a low-rank representation of the error is a randomized SVD, which introduces some degree of stochastic variability into the implementation. The strategy is formulated and implemented in the context of discontinuous Galerkin spatial discretizations of PDEs and applied to several versions of DLRA methods found in the literature as well as a new variant. Numerical experiments comparing the predictor-corrector strategy to other methods demonstrate robustness to overcome shortcomings of step truncation or strict DLRA approaches: The former may require more memory than is strictly needed, while the latter may miss transients solution features that cannot be recovered. The effect of randomization, tolerances, and other implementation parameters is also explored.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Utah FORGE 2-2446: Closing the Loop Between In-Situ Stress Complexity and EGS Fracture Complexity - 2024 Annual Workshop Presentation

This is a presentation on Closing the Loop Between In-Situ Stress Complexity and EGS Fracture Complexity by Lawrence Livermore National Laboratory, presented by Matteo Cusini. The video discusses the combination of high-fidelity simulations and true-triaxial block fracturing tests to explore the intricate relationship between in-situ stress and hydraulic fracture patterns. This presentation was featured in the Utah FORGE R&D Annual Workshop on August 14, 2024.

15 GEOTHERMAL ENERGY↗

DOE OSTI2020

1 K refrigerator for the CLAS12 Polarized Target Design, Construction, and First Results

A dynamically polarized target of protons and deuterons in irradiated NH3 and ND3 will be employed with the CLAS12 detector system to explore the spin structure of the nucleon in Hall B at Jefferson Lab. This target will feature a versatile, horizontal 1 K refrigerator that has been constructed by a collaboration of Christopher Newport University, Old Dominion University, the University of Virginia, and the JLab Target Group. A description of the challenges involved with designing the target for the CLAS12 experiments and the collaboration’s solutions will be presented. These include a modular and compact design of the 1 K refrigerator and its ancillary equipment, as well as a novel mechanism for loading the target samples. Initial test results of the system will also be included.

Brock, James↗

NASA NTRS1983

Substance geology of the western desert in Egypt and Sudan revealed by Shuttle Imaging Radar (SIR-A)

A correlation of known archaeologic sites with the mapped locations of the streamcourses is expected and may lead to new interpretations of early human history in the Sahara. The valley networks, faults, and other subjacent bedrock features mapped on the SIR-A images are promising areas for ground water and mineral exploration. Additionally, the analogies between the interplay of wind and running water in the geologic history of the Sahara and of Mars are strengthened by the SIR-A discoveries of relict drainage systems beneath the eolian veneer of Egypt and Sudan.

Breed, C. S.↗

NASA NTRS1987

Scaling the electromagnetically driven explosive shock simulator

A heavy payload electromagnetically driven explosive shock simulator, referred to as EDESS-3, has been assembled and characterized at the Navel research Weapons Center. EDESS-3 is the logical outgrowth of the earlier EDESS 1 and 2 simulator work which explored the use of electrical pulse power technology for the generation of explosive like shocks. The features of the EDESS-3 are presented, and designs for the next generation of EDESS machines are introduced.

Persh, Robert I.↗

NASA NTRS1989

Taylor instability in rhyolite lava flows

A refined Taylor instability model is developed to describe the surface morphology of rhyolite lava flows. The effect of the downslope flow of the lava on the structures resulting from the Taylor instability mechanism is considered. Squire's (1933) transformation is developed for this flow in order to extend the results to three-dimensional modes. This permits assessing why ridges thought to arise from the Taylor instability mechanism are preferentially oriented transverse to the direction of lava flow. Measured diapir and ridge spacings for the Little and Big Glass Mountain rhyolite flows in northern California are used in conjunction with the model in order to explore the implications of the Taylor instability for flow emplacement. The model suggests additional lava flow features that can be measured in order to test whether the Taylor instability mechanism has influenced the flows surface morphology.

Baum, B. A.↗

NASA NTRS1990

Turbulence in a reacting contact surface

Turbulent features in a shock tube's contact surface with the reversible reaction 2NO2 to N2O4 are explored. Turbulent densities and velocities show an overall power-law dependence in the fluctuation spectra. At fixed reactant percentages, turbulence increases with increasing Reynolds number. At fixed Reynolds numbers, increasing the reactant percentages causes a reduction in turbulence and an increase in the relative strength of discrete high-frequency components in the density fluctuation spectra. The reliability of conventional chemical modeling for this system apparently decreases with increasing turbulence in a manner suggestive of reaction rate distortion, consistent with theoretical speculation.

Johnson, J. A., III↗

NASA NTRS1994

Dante's Volcano

This video contains two segments: one a 0:01:50 spot and the other a 0:08:21 feature. Dante 2, an eight-legged walking machine, is shown during field trials as it explores the inner depths of an active volcano at Mount Spurr, Alaska. A NASA sponsored team at Carnegie Mellon University built Dante to withstand earth's harshest conditions, to deliver a science payload to the interior of a volcano, and to report on its journey to the floor of a volcano. Remotely controlled from 80-miles away, the robot explored the inner depths of the volcano and information from onboard video cameras and sensors was relayed via satellite to scientists in Anchorage. There, using a computer generated image, controllers tracked the robot's movement. Ultimately the robot team hopes to apply the technology to future planetary missions.

Source record↗

NASA NTRS2006

The Australian National Airborne Field Experiment 2005: Soil Moisture Remote Sensing at 60 Meter Resolution and Up

Spatially-distributed soil moisture observations have applications spanning a wide range of spatial resolutions from the very local needs of individual farmers to the progressively larger areas of interest to weather forecasters, water resource managers, and global climate modelers. To date, the most promising approach for space-based remote sensing of soil moisture makes use of passive microwave emission radiometers at L-band frequencies (1-2 GHz). Several soil moisture-sensing satellites have been proposed in recent years, with the European Space Agency's Soil Moisture Ocean Salinity (SMOS) mission scheduled to be launched first in a couple years. While such a microwave-based approach has the advantage of essentially allweather operation, satellite size limits spatial resolution to 10's of km. Whether used at this native resolution or in conjunction with some type of downscaling technique to generate soil moisture estimates on a finer-scale grid, the effects of subpixel spatial variability play a critical role. The soil moisture variability is typically affected by factors such as vegetation, topography, surface roughness, and soil texture. Understanding and these factors is the key to achieving accurate soil moisture retrievals at any scale. Indeed, the ability to compensate for these factors ultimately limits the achievable spatial resolution and/or accuracy of the retrieval. Over the last 20 years, a series of airborne campaigns in the USA have supported the development of algorithms for spaceborne soil moisture retrieval. The most important observations involved imagery from passive microwave radiometers. The early campaigns proved that the retrieval worked for larger and larger footprints, up to satellite-scale footprints. These provided the solid basis for proposing the satellite missions. More recent campaigns have explored other aspects such as retrieval performance through greater amounts of vegetation. All of these campaigns featured extensive ground truth collection over a range of grid spacings, to provide a basis for examining the effects of subpixel variability. However, the native footprint size of the airborne L-band radiometers was always a few hundred meters. During the recently completed (November, 2005) National Airborne Field Experiment (NAFE) campaign in Australia, a compact L-band radiometer was deployed on a small aircraft. This new combination permitted routine observations at native resolutions as high as 60 meters, substantially finer than in previous airborne soil moisture campaigns, as well as satellite footprint areal coverage. The radiometer, the Polarimetric L-band Microwave Radiometer (PLMR) performed extremely well and operations included extensive calibration-related observations. Thus, along with the extensive fine-scale ground truth, the NAFE dataset includes all the ingredients for the first scaling studies involving very-high-native resolution soil moisture observations and the effects of vegetation, roughness, etc. A brief overview of the NAFE will be presented, then examples of the airborne observations with resolutions from 60 m to 1 km will be shown, and early results from scaling studies will be discussed.

Kim, E. J.↗

NASA NTRS2012

An Fe XXIV Absorption Line in the Persistent Spectrum of the Dipping Low-Mass X-Ray Binary 1A 1744-361

We report on Chandra X-ray Observatory (Chandra) High Energy Transmission Grating spectra of the dipping low-mass X-ray binary 1A 1744−361 during its 2008 July outburst. We find that its persistent emission is well modeled by a blackbody (kT approx. 1.0 keV) plus power law (Gamma approx. 1.7) with an absorption edge. In the residuals of the combined spectrum, we find a significant absorption line at 6.961 +/- 0.002 keV, consistent with the Fe xxvi (hydrogen-like Fe) 2-1 transition.We place an upper limit on the velocity of a redshifted flow of nu < 221 km/s. We find an equivalent width for the line of 27+2/−3 eV, from which we determine a column density of (7 +/- 1)×10(exp 17) /sq. cm via a curve-of-growth analysis. Using XSTAR simulations, we place a lower limit on the ionization parameter of >103.6 erg cm/s. We discuss what implications the feature has on the system and its geometry. We also present Rossi X-ray Timing Explorer data accumulated during this latest outburst and, via an updated color-color diagram, clearly show that 1A 1744−361 is an "atoll" source

stars↗

NASA NTRSDate not supplied

On A Higher Order Method for Anonymous Feature Processing

Some feature-driven navigation sources, such as cameras or lidars, often require measurement-to-feature associations between the collected data and an onboard feature catalog to be performed upstream of the filter. Standard navigation practice suggests the use of Kalman updates with measurements that have first passed residual editing tests, but this is often insufficient to prevent updates based upon incorrectly associated data, leading to filter degradation and divergence. Recent work has developed the anonymous feature processing (AFP) technique that eliminates reliance upon explicit feature associations outside of the filter entirely while maintaining desirable estimation performance. This paper continues by exploring the approximation employed by AFP, and a higher order approximation is presented to further improve the estimation performance of the AFP update.

James S Mccabe↗

NASA NTRSDate not supplied

Propagation of the MJO and Associated Moist Dynamics, and the Advantages of Enhanced Resolution in NASA’s GEOS-S2S Forecast System

This presentation explores how reliably the NASA’s new subseasonal to seasonal (S2S) forecast system represents the key features of the Madden-Julian Oscillation (MJO). This system is a fully coupled global model that includes the components of atmosphere, ocean, land, and sea ice. The model runs at an approximate spatial resolution of 0.5 degree for the atmosphere and 0.25 degree for the ocean. It employs a two-moment cloud microphysics to enable aerosol-cloud interaction and implements a novel atmosphere-ocean interface layer to enhance the representation of the diurnal warm and cool-skin layer.

Young-Kwon Lim↗

NASA NTRSDate not supplied

Propagation of the MJO and Associated Moist Dynamics, and the Advantages of Enhanced Resolution in NASA’s GEOS-S2S Forecast System

Young-Kwon Lim↗