Search NASA⌕ Search

SEARCH · Search NASA

Results for “biological processing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,729 records · Page 96
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Urban Scaling as Validation for Predictions of Imperviousness From Population

Abstract Strategies for creating quantitative projections for human systems, especially impervious surfaces, are necessary to consider the human drivers of climate and ecosystem change. There are models that generate predictions of how impervious surfaces may change in response to different potential futures, but few tools exist for validating those predictions. We seek to fill that gap. We demonstrate a statistically robust sublinear scaling relationship between population and urban imperviousness across a 15 year history. We show that Integrated Climate and Land‐Use Scenarios (ICLUS) urbanization projections are also consistent with theory. These results demonstrate a theory that can be used to validate other models' predictions of urban growth and land cover change, analogous to the ways in which allometric scaling laws in biology have been used to validate process‐based models of ecosystem composition under different climate scenarios.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Multi-scale organization in communicating active matter

The emergence of collective motion among interacting, self-propelled agents is a central paradigm in non-equilibrium physics. Examples of such active matter range from swimming bacteria and cytoskeletal motility assays to synthetic self-propelled colloids and swarming microrobots. Remarkably, the aggregation capabilities of many of these systems rely on a theme as fundamental as it is ubiquitous in nature: communication. Despite its eminent importance, the role of communication in the collective organization of active systems is not yet fully understood. Here we report on the multi-scale self-organization of interacting self-propelled agents that locally process information transmitted by chemical signals. We show that this communication capacity dramatically expands their ability to form complex structures, allowing them to self-organize through a series of collective dynamical states at multiple hierarchical levels. Our findings provide insights into the role of self-sustained signal processing for self-organization in biological systems and open routes to applications using chemically driven colloids or microrobots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

ContScout: sensitive detection and removal of contamination from annotated genomes

Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Random heteropolymers as enzyme mimics

Despite successes in replicating the primary–secondary–tertiary structure hierarchy of protein, it remains elusive to synthetically materialize protein functions that are deeply rooted in their chemical, structural and dynamic heterogeneities. We propose that for polymers with backbone chemistries different from that of proteins, programming spatial and temporal projections of sidechains at the segmental level can be effective in replicating protein behaviours; and leveraging the rotational freedom of polymer can mitigate deficiencies in monomeric sequence specificity and achieve behaviour uniformity at the ensemble level. Here, guided by the active site analysis of about 1,300 metalloproteins, we design random heteropolymers (RHPs) as enzyme mimics based on one-pot synthesis. We introduce key monomers as the equivalents of the functional residues of protein and statistically modulate the chemical characteristics of key monomer-containing segments, such as segmental hydrophobicity. The resultant RHPs form pseudo-active sites that provide key monomers with protein-like microenvironments, co-localize substrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and cyclization of citronellal with isopulegol/menthoglycol selectivity. This RHP design led to enzyme-like materials that can retain catalytic activity under non-biological conditions, are compatible with scalable processing and have expanded substrate scope, including environmentally long-lasting antibiotic tetracycline.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Abstract The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Proton transfer in acetaldehyde–water clusters mediated by a single water molecule

Proton transfer in aqueous media is a ubiquitous process, occurring in acid–base chemistry, biology, and in atmospheric photochemistry. Photoionization mass spectrometry coupled with theoretical calculations demonstrate that a relay-type proton transfer mechanism is operational for single-water-molecule-assisted proton transfer between two acetaldehyde molecules in the gas phase. Threshold photoionization of acetaldehyde–water clusters leads to proton transfer between the formyl groups (–CH=O) of one acetaldehyde molecule to another, and the subsequent formation of cationic moieties. Density functional theory computations reveal several plausible pathways of proton transfer in mixed cluster cations. Among these pathways, water-mediated proton transfer is energetically favored. Finally, mass spectra and photoionization efficiency curves confirm these theoretical findings and also demonstrate the increased stability of cluster cations where acetaldehyde molecules are symmetrically bonded to the hydronium ion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Pursuing theranostics: a multimodal architecture approach

Theranostics is a field of nuclear medicine which uses the same targeting vector and chelating system for both a diagnostic and therapeutic radionuclide, allowing for uniformity in imaging and treatment.

Bender, Aidan A. [Nuclear Engineering Program, Uni↗
DOE OSTI2014

Influence of finite geometrical asymmetry of the electrodes in capacitively coupled radio frequency plasma

Capacitively coupled radio frequency (CCRF) plasmas are widely studied in last decades due to the versatile applicability of energetic ions, chemically active species, radicals, and also energetic neutral species in many material processing fields including microelectronics, aerospace, and biology. A dc self-bias is known to generate naturally in geometrically asymmetric CCRF plasma because of the difference in electrode sizes known as geometrical asymmetry of the electrodes in order to compensate electron and ion flux to each electrode within one rf period. The plasma series resonance effect is also come into play due to the geometrical asymmetry and excited several harmonics of the fundamental in low pressure CCRF plasma. In this work, a 13.56 MHz CCRF plasma is studied on the based on the nonlinear global model of asymmetric CCRF discharge to understand the influences of finite geometrical asymmetry of the electrodes in terms of generation of dc self-bias and plasma heating. The nonlinear global model on asymmetric discharge has been modified by considering the sheath at the grounded electrode to taking account the finite geometrical asymmetry of the electrodes. The ion density inside both the sheaths has been taken into account by incorporating the steady-state fluid equations for ions considering that the applied rf frequency is higher than the typical ion plasma frequency. Details results on the influences of geometrical asymmetry on the generation of dc self-bias and plasma heating are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Design strategies for self-assembly of discrete targets

Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks to hierarchical sequences of intermediates, all the way to the fully addressable limit in which each component is unique. In this paper, we introduce an idealized model of cubic particles with patterned faces that allows self-assembly strategies to be compared and tested. We consider a simple octameric target, starting with the minimal requirements for successful self-assembly and comparing the benefits and limitations of more sophisticated hierarchical and addressable schemes. Simulations are performed using a hybrid dynamical Monte Carlo protocol that allows self-assembling clusters to rearrange internally while still providing Stokes-Einstein-like diffusion of aggregates of different sizes. Our simulations explicitly capture the thermodynamic, dynamic, and steric challenges typically faced by self-assembly processes, including competition between multiple partially completed structures. Self-assembly pathways are extracted from the simulation trajectories by a fully extendable scheme for identifying structural fragments, which are then assembled into history diagrams for successfully completed target structures. For the simple target, a one-component assembly scheme is most efficient and robust overall, but hierarchical and addressable strategies can have an advantage under some conditions if high yield is a priority.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Electronic structures and binding motifs of sodium polysulfide clusters NaSn- (n = 5-9): a joint negative ion photoelectron spectroscopy and computational investigation

Motivated by the significant biological functions of polysulfides in life processes and important applications of sodium polysulfides in battery sciences, herein we report a joint experimental and computational study on the electronic and geometric structures of a series of NaSn- (n = 5-9) clusters. The cryogenic, size-selective, negative ion photoelectron spectroscopy (NIPES) is employed to obtain their photoelectron spectra, in which distinctive spectral features with electron binding energy (EBE) up to 6.4 eV are unraveled. The EBE of the first peak in each spectrum for NaSn- (n =5-9), assigned to the transition from the ground state of anion to the ground state of each neutral radical, is observed to increase with cluster size. The vertical detachment energies (VDEs), determined from the first peak maximum, are 3.43 ± 0.02, 3.57 ± 0.02, 3.82 ± 0.03, 3.86 ± 0.02, and 4.00 ± 0.02 eV and the adiabatic detachment energies (ADEs), determined by the onset of the first peak, are 3.27 ± 0.05, 3.44 ± 0.05, 3.65 ± 0.05, 3.75 ± 0.05, and 3.93 ± 0.05 eV, for n = 5-9, respectively. A plural of low-lying isomers of anions are screened and identified with density functional theory calculations, showing that all featuring preference for a chain-like polysulfide moiety electrostatically interacted with a sodium cation. The calculated VDEs and ADEs using the high-level CCSD(T)/aug-cc-pVTZ method are in excellent agreement with experimental results, further confirming the identified isomers as most stable ones. Further analyses based on the excited-state transition, molecular orbitals and natural population charge are performed to assign all observed spectral bands along the binding energy axis, suggesting that the electron detachment process and observed excitations mainly derived from the polysulfide chain of NaSn- clusters. This work provides a fundamental understanding of the intrinsic molecular properties of sodium polysulfide systems, which widely exist in life science and sodium-sulfur cells.

Li, Zhipeng↗
DOE OSTI2022

CHESS: The future direct geometry spectrometer at the second target station

CHESS, chopper spectrometer examining small samples, is a planned direct geometry neutron chopper spectrometer designed to detect and analyze weak signals intrinsic to small cross sections (e.g., small mass, small magnetic moments, or neutron absorbing materials) in powders, liquids, and crystals. CHESS is optimized to enable transformative investigations of quantum materials, spin liquids, thermoelectrics, battery materials, and liquids. The broad dynamic range of the instrument is also well suited to study relaxation processes and excitations in soft and biological matter. The 15 Hz repetition rate of the Second Target Station at the Spallation Neutron Source enables the use of multiple incident energies within a single source pulse, greatly expanding the information gained in a single measurement. Furthermore, the high flux grants an enhanced capability for polarization analysis. This enables the separation of nuclear from magnetic scattering or coherent from incoherent scattering in hydrogenous materials over a large range of energy and momentum transfer. This paper presents optimizations and technical solutions to address the key requirements envisioned in the science case and the anticipated uses of this instrument.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

X-rays put molecules into a spin

The past decade has witnessed the emergence of a new X-ray light source technology that has been under development for some decades: the so-called self-amplified spontaneous emission-based free-electron laser (FEL). Furthermore, such lasers provide pulses with durations from just below 1 fs (10 –15 s) to over 100 fs and with energies from a few microjoules to a few millijoules, permitting the study of, for example, nonlinear optical effects (1), ultrafast processes (2), coherent diffractive imaging of biological systems such as protein crystals (3, 4), and mimivirus (5). After the opening of the first extreme-UV to soft X-ray user facility, namely FLASH in the Deutsches Elektronen-Synchrotron at Hamburg, Germany (6), a number of other machines covering the extreme-UV (FERMI FEL-1, DALIAN), soft X-ray (FERMI FEL-2, FLASH1/FLASH2), and hard X-ray spectral ranges (LCLS, PAL-XFEL, SACLA, and XFEL) have been opened to users from a wide range of scientific and engineering disciplines.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Down-regulation of kelch domain-containing F-box protein in Arabidopsis enhances the production of (poly)phenols and tolerance to ultraviolet radiation

Phenylpropanoid biosynthesis in plants engenders myriad phenolics with diverse biological functions. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway, directing primary metabolic flux into a phenylpropanoid branch. Previously, we demonstrated that the Arabidopsis Kelch-domain containing F-box proteins, AtKFB01, -20, and -50, function as the negative regulators controlling phenylpropanoid biosynthesis via mediating PAL’s ubiquitination and subsequent degradation. Here, we reveal that Arabidopsis KFB39, a close homolog of AtKFB50, also interacts physically with PAL isozymes and modulates PALs' stability and activity. Disturbing the expression of KFB39 reciprocally affects the accumulation/deposition of a set of phenylpropanoid end products, suggesting that KFB39 is an additional post-translational regulator responsible for the turnover of PAL and negatively controlling phenylpropanoid biosynthesis. Furthermore, we discover that exposure of Arabidopsis to UV-B radiation suppresses the expression of all four KFB genes while inducing the transcription of PAL isogenes; these data suggest that Arabidopsis consolidates both transcriptional and post-translational regulation mechanisms to maximize its responses to UV stress. Simultaneous down-regulation of all four identified KFBs significantly enhances the production of (poly)phenols and the plant’s tolerance to UV irradiation. This study offers a biotechnological approach for engineering the production of useful phenolic chemicals and for increasing a plant’s resistance to environmental stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High-resolution cryo-EM reconstructions in the presence of substantial aberrations

Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula quantifying information loss owing to their presence is inferred that explains why Fourier-shell coefficient-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. The analysis is validated with reference-based aberration refinement for two cryo-EM SPR data sets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively, were obtained. The results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher order aberrations, and address inconsistent guidelines regarding the level of aberrations that is acceptable in cryo-EM SPR experiments.

3D reconstruction and image processing↗