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At least 217 records · Page 12

Perspectives for self-driving labs in synthetic biology

Self-driving labs (SDLs) combine fully automated experiments and data collection with artificial intelligence (AI) and control algorithms that decide not only the set of parameters for the next experiment, but also potentially which scientific hypotheses to test. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. Whereas there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single, easily accessible, target for affecting the incredibly wide repertoire of biological cell behavior. Since they can provide large amounts of high-quality data, SDLs can be a platform for AI to develop approaches to systematically convert data into scientific knowledge systems. These knowledge systems can be used both to understand the biological world and to design bioengineered systems to fit a desired specification (inverse design). However, the level of investment required for the creation of biological SDLs is only warranted if directed towards solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

The LuNaMaps Project: Advancing Capabilities for Developing and Validating Digital Elevation Models of Rocky Surfaces from Orbital Data

Both navigation and surface science can benefit from the ability to generate high resolution and accurate maps of the surface of the Moon and other solar system bodies. The primary way these maps are generated is through the use of orbital imagery and ranging data. Traditionally, the process of using orbital imagery and ranging data is tedious and labor-intensive. Additionally, once maps have been built, there has generally been limited effort in developing standards by which to verify the accuracy and quality of the generated maps. The Lunar Navigation Maps (LuNaMaps) project is a NASA Game Changing Development (GCD) project which over the last 4 years has aimed to address these issues both for the Moon and for other rocky solar system bodies. This has been accomplished through development of new and existing capabilities including: a suite of methods and tools to combine all sources of orbital imagery; a benchmark data set as well as basic requirements for high-fidelity simulations of precision landing functions; tools to synthetically enhance map products with lander-scale features for use in the development and testing of hazard detection systems; methods and tools to evaluate the accuracy of developed digital elevation maps (DEMs) and their quality for use in terrain relative navigation scenarios; and tools to realistically render image and lidar data. In this work, we provide an overview of the capabilities developed through LuNaMaps, demonstrating its use for processing existing lunar data, and describing how it can be applied to other use cases. We additionally provide preliminary results showing the application of the developed tools and processes to the generation of elevation maps of the Lunar Surface Proving Grounds (LSPG) lunar analog at Astrobotic’s Mojave testing facility using “orbital imagery” captured by a drone. In this terrestrial demonstration, we have the benefit of being able to compare the results to a ground truth model of the LSPG. We finally describe plans to use the newly created maps in a terrestrial terrain relative navigation demonstration over the LSPG in early 2025.

optical navigation↗

Predictive Self-Healing Seals for Gas Transmission

Damaged elastomeric diaphragms within pneumatic controllers used in the oil and gas industry lead to an unintended release of methane. Self-healing microvascular materials capable of healing various types of damage have been fabricated. These microvascular materials are designed to replace currently available commercial diaphragms found in pneumatic controllers and provide a solution to reduce unintended methane leaks. This project demonstrated the ability of these materials to reduce methane release by more than 80% in lab and pilot settings. Additionally, ML approaches successfully identified leaking systems based on training using synthetic and real data.

03 NATURAL GAS↗

The Laboratory for Oceans Computing Facility

The first VAX computer in the Laboratory for Oceans Computing Facility (LOCF) was installed and the facility was largely expanded. The growth is not only in hardware and software, but also in the number of users and in supporting research and development projects. The LOCF serves as a general purpose computing facility for: ocean color research projects, sea ice research projects, processing of the Nimbus-7 Coastal Zone Color Scanner data set, real time ingest and analysis of TIROS-N satellite data, study of the Synthetic Aperture Radar data, study of LANDSAT data, and many others. The physical space and the electrical power layout of the computing room were modified to accommodate all the equipment. The LOCF has several image processing stations which include two International Imaging Systems (IIS) model 75 processors and one Adage processor. The facility has the capability of ingesting the TIROS-N HRPT satellite data on a real time basis. More than 30 software packages were installed on the systems. System software packages, network software, FORTRAN and C compilers, database management software, image processing software, graphics, mathematics and statistics packages, TAE, Catalog Manager, GEMPAK, LAS and many other software developed on the LOCF computers such as SEAPAK have greatly advanced the capability of the LOCF.

Kao, R.↗

Sequential Selection for Minimizing the Variance with Application to Crystallization Experiments

For many crystal-based products (e.g., pharmaceuticals, energy storage), the size uniformity is not only a key quality attribute, but sometimes also an indicator of other attributes such as solid purity. This article proposes a sequential selection approach to find a proper experimental setting that leads to high uniformity, or equivalently, small variance for crystal sizes, from the advanced slug flow reaction crystallization process of a model crystal, called manganese oxalate hydrate. The proposed sequential selection approach contains a Bayesian adaptive method to incorporate new uniformity measurements in each step and two design acquisition functions to improve the selection of the most promising experimental setting in terms of minimizing the variance. We study the performance of the proposed approach through multiple synthetic numerical studies, as well as a case study based on data from slug flow crystallization experiments. Throughout these studies, the proposed approach shows competitive performance in identifying the best experimental setting.

Expected improvement↗

Utilizing Environmental Tracers to Reduce Groundwater Flow and Transport Model Parameter Uncertainties

Abstract Non‐uniqueness in groundwater model calibration is a primary source of uncertainty in groundwater flow and transport predictions. In this study, we investigate the ability of environmental tracer information to constrain groundwater model parameters. We utilize a pilot point calibration procedure conditioned to subsets of observed data including: liquid pressures, tritium ( 3 H), chlorofluorocarbon‐12 (CFC‐12), and sulfur hexafluoride (SF 6 ) concentrations; and groundwater apparent ages inferred from these environmental tracers, to quantify uncertainties in the heterogeneous permeability fields and infiltration rates of a steady‐state 2‐D synthetic aquifer and a transient 3‐D model of a field site located near Riverton, Wyoming (USA). To identify the relative data worth of each observation data type, the post‐calibration uncertainties of the optimal parameters for a given observation subset are compared to that from the full observation data set. Our results suggest that the calibration‐constrained permeability field uncertainties are largest when liquid pressures are used as the sole calibration data set. We find significant reduction in permeability uncertainty and increased predictive accuracy when the environmental tracer concentrations, rather than apparent groundwater ages, are used as calibration targets in the synthetic model. Calibration of the Riverton field site model using environmental tracer concentrations directly produces infiltration rate estimates with the lowest uncertainties, however; permeability field uncertainties remain similar between the environmental tracer concentration and apparent groundwater age calibration scenarios. This work provides insight on the data worth of environmental tracer information to calibrate groundwater models and highlights potential benefits of directly assimilating environmental tracer concentrations into model parameter estimation procedures.

54 ENVIRONMENTAL SCIENCES↗

KilonovaNet : Surrogate models of kilonova spectra with conditional variational autoencoders

ABSTRACT Detailed radiative transfer simulations of kilonova spectra play an essential role in multimessenger astrophysics. Using the simulation results in parameter inference studies requires building a surrogate model from the simulation outputs to use in algorithms requiring sampling. In this work, we present kilonovanet, an implementation of conditional variational autoencoders (cVAEs) for the construction of surrogate models of kilonova spectra. This method can be trained on spectra directly, removing overhead time of pre-processing spectra, and greatly speeds up parameter inference time. We build surrogate models of three state-of-the-art kilonova simulation data sets and present in-depth surrogate error evaluation methods, which can in general be applied to any surrogate construction method. By creating synthetic photometric observations from the spectral surrogate, we perform parameter inference for the observed light-curve data of GW170817 and compare the results with previous analyses. Given the speed with which kilonovanet performs during parameter inference, it will serve as a useful tool in future gravitational wave observing runs to quickly analyse potential kilonova candidates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The Last Journey. I. An Extreme-scale Simulation on the Mira Supercomputer

The Last Journey is a large-volume, gravity-only, cosmological N-body simulation evolving more than 1.24 trillion particles in a periodic box with a side length of 5.025 Gpc. It was implemented using the HACC simulation and analysis framework on the BG/Q system Mira. The cosmological parameters are chosen to be consistent with the results from the Planck satellite. A range of analysis tools have been run in situ to enable a diverse set of science projects and, at the same time, keep the resulting data amount manageable. Analysis outputs have been generated starting at redshift z ~ 10 to allow for construction of synthetic galaxy catalogs using a semianalytic modeling approach in postprocessing. As part of our in situ analysis pipeline, we employ a new method for tracking halo substructures, introducing the concept of subhalo cores. The production of multiwavelength synthetic sky maps is facilitated by generating particle light cones in situ, also beginning at z ~ 10. We provide an overview of the simulation setup and generated data products; a first set of analysis results is presented. A subset of the data is publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗

Determining the leading-order contact term in neutrinoless double β decay

We present a method to determine the leading-order (LO) contact term contributing to the nn → ppe - e - amplitude through the exchange of light Majorana neutrinos. Our approach is based on the representation of the amplitude as the momentum integral of a known kernel (proportional to the neutrino propagator) times the generalized forward Compton scattering amplitude n ( p 1 ) n ( p 2 ) W + ( k ) → \( p\left({p}_1^{\prime}\right)p\left({p}_2^{\prime}\right){W}^{-}(k) \) , in analogy to the Cottingham formula for the electromagnetic contribution to hadron masses. We construct model-independent representations of the integrand in the low- and high-momentum regions, through chiral EFT and the operator product expansion, respectively. We then construct a model for the full amplitude by interpolating between these two regions, using appropriate nucleon factors for the weak currents and information on nucleon-nucleon ( NN ) scattering in the 1 S 0 channel away from threshold. By matching the amplitude obtained in this way to the LO chiral EFT amplitude we obtain the relevant LO contact term and discuss various sources of uncertainty. We validate the approach by computing the analog I = 2 NN contact term and by reproducing, within uncertainties, the charge-independence-breaking contribution to the 1 S 0 NN scattering lengths. While our analysis is performed in the \( \overline{\mathrm{MS}} \) scheme, we express our final result in terms of the scheme-independent renormalized amplitude \( {\mathcal{A}}_{\nu}\left(\left|\mathbf{p}\right|,\left|\mathbf{p}^{\prime}\right|\right) \) at a set of kinematic points near threshold. We illustrate for two cutoff schemes how, using our synthetic data for \( {\mathcal{A}}_{\nu } \) , one can determine the contact-term contribution in any regularization scheme, in particular the ones employed in nuclear-structure calculations for isotopes of experimental interest.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On the Impact Angle of Hurricane Sandy's New Jersey Landfall

Hurricane Sandy's track crossed the New Jersey coastline at an angle closer to perpendicular than any previous hurricane in the historic record, one of the factors contributing to recordsetting peak-water levels in parts of New Jersey and New York. To estimate the occurrence rate of Sandy-like tracks, we use a stochastic model built on historical hurricane data from the entire North Atlantic to generate a large sample of synthetic hurricanes. From this synthetic set we calculate that under long-term average climate conditions, a hurricane of Sandy's intensity or greater (category 1+) makes NJ landfall at an angle at least as close to perpendicular as Sandy's at an average annual rate of 0.0014 yr-1 (95% confidence range 0.0007 to 0.0023); i.e., a return period of 714 years (95% confidence range 435 to 1429).

hurricanes↗

Measured and Simulated Acoustic Signature of a Full-Scale Aircraft with Airframe Noise Reduction Technology Installed

Microphone phased-array and pole-mounted microphone data gathered during the NASA Acoustics Research Measurements flight tests were used to benchmark results from companion full-scale aeroacoustics simulations. Conducted with the lattice Boltzmann solver PowerFLOW®, the simulations predicted the acoustic behavior of various tested aircraft configurations. Emphasis was placed on those flown during the third flight test - a Fowler flap-equipped Gulfstream G-III with and without noise abatement technology on the main landing gear. Direct comparisons between experimental and synthetic microphone phasedarray data were achieved by applying the same processing and deconvolution technique to both sets of data. To extend the validation of the computations to the metric used for noise certification, the Effective Perceived Noise Level, a high-fidelity digital model of the nose landing gear, which was excluded from earlier computations, was developed and integrated into the G-III aircraft geometry. The acoustic study presented here demonstrates that the simulated beamform maps and corresponding integrated farfield spectra accurately predict the locations and strengths of the prominent airframe noise sources present on the G-III aircraft.

Khorrami, Mehdi R.↗

TPSAS-NF1676L-27509-DND

The information about composition of aerosols has a great importance for monitoring and understanding of climate and environment dynamics. Such information can be obtained using situ measurements or chemical transport models. However, in situ sampling has limited spatial and temporal coverage, while estimations have large uncertainties. The present work enables the monitoring of aerosol chemical species from space-borne observations, providing observationally-based results with spatial and temporal coverage. Following the ideas of Schuster et al.(2005, 2009, 2016), we retrieve chemical composition directly from satellite observations without intermediate retrieval of the refractive index (in contrast with Schuster's approach). This approach is expected to reduce the influence of modeling uncertainties, and to provide additional constraints in situations where remote sensing observations do not have enough spectral sensitivity to refractive index. One of principal difficulties is the identification of an adequate model for linking refractive index to chemical composition. Therefore, the initial effort of this work has focused on identifying an optimal physico-chemistry to refractive index conversion model. With that purpose, we first tested the retrieval approach using a simplified volume-weighting model and updated by the Maxwell Garnett mixing model. This concept was incorporated into the GRASP algorithm designed to retrieve an extended set of atmospheric parameters from remote sensing observations. Then a series of sensitivity tests using synthetic data of POLDER/PARASOL were conducted, and followed by inversion of real PARASOL observations over Africa. The sensitivity tests showed that these two models allow the retrieval to distinguish amongst the assumed chemical species. Results obtained from real PARASOL data demonstrated good agreement with the optical characteristics provided by AERONET. In addition, the obtained patterns of chemical component distribution agreed with known physical expectations. We also compared the chemical composition retrievals to GOCART model simulations and obtained good consistencies.

Lei Li↗

Nimbus 7 earth radiation budget wide field of view climate data set improvement. I - The earth albedo from deconvolution of shortwave measurements

A deconvolution method for extracting the top of the atmosphere (TOA) mean, daily albedo field from a set of wide-FOV (WFOV) shortwave radiometer measurements is proposed. The method is based on constructing a synthetic measurement for each satellite observation. The albedo field is represented as a truncated series of spherical harmonic functions, and these linear equations are presented. Simulation studies were conducted to determine the sensitivity of the method. It is observed that a maximum of about 289 pieces of data can be extracted from a set of Nimbus 7 WFOV satellite measurements. The albedos derived using the deconvolution method are compared with albedos derived using the WFOV archival method; the developed albedo field achieved a 20 percent reduction in the global rms regional reflected flux density errors. The deconvolution method is applied to estimate the mean, daily average TOA albedo field for January 1983. A strong and extensive albedo maximum (0.42), which corresponds to the El Nino/Southern Oscillation event of 1982-1983, is detected over the south central Pacific Ocean.

Hucek, Richard R.↗

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗

SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R g ), pair distance distribution function (PDDF)-derived R g , maximum particle dimension (D max ), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R g agreement, an important indicator of well-measured data sets. For assistance in D max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R 2 = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

36 MATERIALS SCIENCE↗

Neural network denoising of x-ray images from high-energy-density experiments

Noise is a consistent problem for x-ray transmission images of High-Energy-Density (HED) experiments because it can significantly affect the accuracy of inferring quantitative physical properties from these images. We consider experiments that use x-ray area backlighting to image a thin layer of opaque material within a physics package to observe its hydrodynamic evolution. The spatial variance of the x-ray transmission across the system due to changing opacity serves as an analog for measuring density in this evolving layer. The noise in these images adds nonphysical variations in measured intensity, which can significantly reduce the accuracy of our inferred densities, particularly at small spatial scales. Denoising these images is thus necessary to improve our quantitative analysis, but any denoising method also affects the underlying information in the image. In this paper, we present a method for denoising HED x-ray images via a deep convolutional neural network model with a modified DenseNet architecture. In our denoising framework, we estimate the noise present in the real (data) images of interest and apply the inferred noise distribution to a set of natural images. These synthetic noisy images are then used to train a neural network model to recognize and remove noise of that character. We show that our trained denoiser network significantly reduces the noise in our experimental images while retaining important physical features.

47 OTHER INSTRUMENTATION↗

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model

The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.

59 BASIC BIOLOGICAL SCIENCES↗