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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Relaxation behavior in low-frequency complex conductivity of sands caused by bacterial growth and biofilm formation by Shewanella oneidensis under a high-salinity condition

Complex electrical conductivity is increasingly used to monitor subsurface processes associated with microbial activities because microbial cells mostly have surface charges and thus electrical double layers. Although highly saline environments are frequently encountered in coastal and marine sediments, there are limited data available on the complex conductivity associated with microbial activities under a high-salinity condition. Therefore, we have developed the spectral responses of complex conductivity of sand associated with bacterial growth and biofilm formation under a highly saline condition of approximately 1% salinity and approximately 2 S/m pore water conductivity with an emphasis on relaxation behavior. A column test is performed, in which the model bacteria Shewanella oneidensis MR-1 are stimulated for cell growth and biofilm formation in a sand pack, whereas the complex conductivity is monitored from 0.01 Hz to 10 kHz. The test results indicate that the real conductivity increases in the early stage due to the microbial metabolites and the increased surface conduction with cell growth but soon begin to decrease because of the reduction of charge passages due to bioclogging. However, the imaginary conductivity significantly increases with time, and clear bell-shaped relaxation behaviors are observed with the peak frequency of 0.1–1 Hz, associated with the double-layer polarization of cells and electrically conductive pili and biofilms. The Cole-Cole relaxation model appears to capture such relaxation behaviors well, and the modeling results indicate gradual increases in normalized chargeability and decreases in relaxation time during bacterial growth and biofilm formation in the highly saline condition. Comparison with previous literature confirms that the high-salinity condition further increases the normalized chargeability, whereas it suppresses the phase shift and thus the imaginary conductivity. Our results suggest that the complex conductivity can effectively capture microbial biomass formation in sands under a highly saline condition.

58 GEOSCIENCES↗
DOE OSTI2020

Effects on Human Non-Small Lung Cancer Cell growth of Cu(II), Au(III) and Re(I) Complexes Containing N-donor Pyridyl Ligands: A Senior Undergraduate Research Project

Hands-on synthetic laboratory experiences are critically important for undergraduate chemistry majors. A senior undergraduate research experience at the College of Wooster is presented in the current work. The inorganic complexes [Cu(phenan) 2 (NO 3 ) 2 ] (1; phenan = phenanthridine) and [Au(phenan)Cl 3 ](2) were prepared by metallation of the phenan ligand in a 1:1 CH 3 OH/CH 2 Cl 2 mixture at room temperature. Complex 1 is a new inorganic coordination compound. The structures were confirmed by X-ray crystallography. Complex 1 reveals a distorted octahedral geometry around the central Cu (II) metal ion. In complex 2, the Au(III) atom exhibits a square planar geometry. In addition, we investigated [Cu(dmeobpy)(H 2 O) 2 ][NO 3 ] 2 (3; dmeobpy = 4,4’-dimethoxy-2,2’-bipyridine), [Cu(bap)(NO 3 ) 2 ](4; bap = 2,6-bis(azaindole)pyridine) and [Re(CO) 3 (dmeobpy)Cl] (5). The cytoxocities of 1-5, phenan, dmeobpy, bap and cisplatin were evaluated against several human non-small cell lung cancer cell lines (NCI-H1975, HCC827, NCI-H460, and NCI-A549). Compound 1 exhibited modest antitumor activity against the HCC827 cell line, with an IC 50 value of 19 µM. Compound 3 exhibits lower cytotoxic activity than 1. Finally, the cytotoxic activity of complex 5 (IC 50 < 11 µM) is significantly greater than 1 and 3 against the H1975 cancer cell line.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Eligibility Assessment of TA-52-1 and TA-52-11: The Ultra-High Temperature Reactor Experiment (UHTREX) Complex

The U.S. Department of Energy (DOE), National Nuclear Security Administration, Los Alamos Field Office (NA-LA) requests the State Historic Preservation Officer (SHPO) to concur with the eligibility determinations contained in this report for Buildings 1 and 11 in Technical Area 52 (TA-52) at Los Alamos National Laboratory (LANL or the Laboratory). Triad National Security LLC cultural resources staff have completed the evaluation of two buildings, called the UHTREX Complex, for inclusion in the National Register of Historic Places (Register). This complex includes the UHTREX Reactor Building (TA-52-1), and an associated Mechanical Assembly Building (TA-52-11). As part of LANL’s Footprint Reduction Program, both facilities of the UHTREX Complex are scheduled for characterization and demolition. In addition to evaluating their eligibility in the Register, the properties at TA-52 were assessed for potential adaptive reuse, long-term preservation, and public interpretation. Based on the findings in this assessment report, both TA-52-1 and TA-52-11 have been determined to not be eligible for inclusion in the Register. The history of the UHTREX Complex lacks association with exceptionally significant Cold War events of scientific developments. Both TA-52-1 and TA-52-11 lack the necessary internal historic integrity suitable for long-term preservation or public interpretation. And both facilities contain legacy radioactive contamination, which prohibits their reuse. In addition to its loss of integrity and context, TA-52- 11 has been determined ineligible due to its status as a support building of secondary or minor importance. In compliance with Section 106 and Section 110 of the National Historic Preservation Act of 1966, as amended, and with the Programmatic Agreement among the U.S. Department of Energy, National Nuclear Security Administration, Los Alamos Field Office, the New Mexico State Historic Preservation Office, and the Advisory Council on Historic Preservation Concerning Management of the Historic Properties at Los Alamos National Laboratory, Los Alamos, New Mexico, the SHPO is requested to concur with the eligibility determinations contained in this report for the UHTREX Complex in TA-52.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Deep Learning Prediction of Protein Complex Structures

Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Predictive Complexity of Quantum Subsystems

We define predictive states and predictive complexity for quantum systems composed of distinct subsystems. This complexity is a generalization of entanglement entropy. It is inspired by the statistical or forecasting complexity of predictive state analysis of stochastic and complex systems theory but is intrinsically quantum. Predictive states of a subsystem are formed by equivalence classes of state vectors in the exterior Hilbert space that effectively predict the same future behavior of that subsystem for some time. As an illustrative example, we present calculations in the dynamics of an isotropic Heisenberg model spin chain and show that, in comparison to the entanglement entropy, the predictive complexity better signifies dynamically important events, such as magnon collisions. It can also serve as a local order parameter that can distinguish long and short range entanglement.

Asplund, Curtis T. (ORCID:0000000305575850)↗
DOE OSTI2022

Scalable Simulation of Pressure Gradient-Driven Transport of Rarefied Gases in Complex Permeable Media Using Lattice Boltzmann Method

Accurate representations of slip and transitional flow regimes present a challenge in the simulation of rarefied gas flow in confined systems with complex geometries. In these regimes, continuum-based formulations may not capture the physics correctly. This work considers a regularized multi-relaxation time lattice Boltzmann (LB) method with mixed Maxwellian diffusive and halfway bounce-back wall boundary treatments to capture flow at high Kn. The simulation results are validated against atomistic simulation results from the literature. We examine the convergence behavior of LB for confined systems as a function of inlet and outlet treatments, complexity of the geometry, and magnitude of pressure gradient and show that convergence is sensitive to all three. The inlet and outlet boundary treatments considered in this work include periodic, pressure, and a generalized periodic boundary condition. Compared to periodic and pressure treatments, simulations of complex domains using a generalized boundary treatment conserve mass but require more iterations to converge. Convergence behavior in complex domains improves at higher magnitudes of pressure gradient across the computational domain, and lowering the porosity deteriorates the convergence behavior for complex domains.

42 ENGINEERING↗
DOE OSTI2022

A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

3DRISM↗
DOE OSTI2026

ODIN: Characterizing the Three-dimensional Structure of Two Protocluster Complexes at z = 3.1

We present a detailed study of the 3D morphology of two extended associations of multiple protoclusters at z = 3.1. These protocluster "complexes," designated COSMOS-z3.1-A and COSMOS-z3.1-C, are the most prominent overdensities of z = 3.1 Lyα emitters (LAEs) identified in the COSMOS field by the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey. These protocluster complexes have been followed up with extensive spectroscopy from Keck, Gemini, and DESI. Using a probabilistic method that combines photometrically selected and spectroscopically confirmed LAEs, we reconstruct the 3D structure of these complexes on scales of ≈50 cMpc. We validate our reconstruction method using the IllustrisTNG300-1 cosmological hydrodynamical simulation and show that it consistently outperforms approaches relying solely on spectroscopic data. The resulting 3D maps reveal that both complexes are irregular and elongated along a single axis, emphasizing the impact of sightline on our perception of structure morphology. The complexes consist of multiple density peaks, 10 in COSMOS-z3.1-A and 4 in COSMOS-z3.1-C. The former is confirmed to be a proto-supercluster, similar to Hyperion at z = 2.4 but observed at an even earlier epoch. Multiple "tails" connected to the cores of the density peaks are seen, likely representing cosmic filaments feeding into these extremely overdense regions. The 3D reconstructions further provide strong evidence that Lyα blobs preferentially reside in the outskirts of the highest density regions. Descendant mass estimates of the density peaks suggest that COSMOS-z3.1-A and COSMOS-z3.1-C will evolve to become ultramassive structures by z = 0, with total masses log ( M / M ,⊙ ,) ≳ 15.3 , exceeding that of Coma.

Ramakrishnan, Vandana [Purdue U., West Lafayette] ↗
DOE OSTI2024

MSD CoP Webinar: Confronting Climate Change Complexity: Intersectionality, Integration, and Innovative Governance

Context: This webinar was hosted by the MultiSector Dynamics Community of Practice (MSD CoP; https://multisectordynamics.org). Abstract: Climate impacts increasingly unfold in interlinked systems of people, nature, and infrastructure. The cascading consequences are revealing sometimes surprising connections, and prospects for climate responses also depend on complex interactions. In this presentation, we will introduce key findings from the United States Fifth National Climate Assessment and build upon them to suggest a framework for understanding and responding to complex climate challenges. This approach involves: (1) integration of disciplines and expertise to understand how intersectionality shapes complex climate impacts and the wide-ranging effects of climate responses, (2) collaborations among diverse knowledge holders to improve responses and better encompass intersectionality, and (3) sustained experimentation with and learning about governance approaches capable of handling the complexity of climate change. We outline actionable steps for climate research to incorporate these pillars, as is increasingly necessary for confronting climate complexity and sustaining equitable, ideally vibrant climate futures. Presenters : Katharine J. Mach, Kripa Jagannathan, Carlos E. Martín, and Linda Shi Moderator: Pat M. Reed (MSD CoP Facilitation Team) This webinar was held on: March 28th, 2024 from 1-2 PM ET

Mach, Katharine J.↗
NASA NTRS1976

Apollo Experiment Report: Lunar-Sample Processing in the Lunar Receiving Laboratory High-Vacuum Complex

A high-vacuum complex composed of an atmospheric decontamination system, sample-processing chambers, storage chambers, and a transfer system was built to process and examine lunar material while maintaining quarantine status. Problems identified, equipment modifications, and procedure changes made for Apollo 11 and 12 sample processing are presented. The sample processing experiences indicate that only a few operating personnel are required to process the sample efficiently, safely, and rapidly in the high-vacuum complex. The high-vacuum complex was designed to handle the many contingencies, both quarantine and scientific, associated with handling an unknown entity such as the lunar sample. Lunar sample handling necessitated a complex system that could not respond rapidly to changing scientific requirements as the characteristics of the lunar sample were better defined. Although the complex successfully handled the processing of Apollo 11 and 12 lunar samples, the scientific requirement for vacuum samples was deleted after the Apollo 12 mission just as the vacuum system was reaching its full potential.

White, D. R.↗
NASA NTRS1979

Prebiotic coordination chemistry: The potential role of transition-metal complexes in the chemical evolution

In approaching the extremely involved and complex problem of the origin of life, consideration of the coordination chemistry appeared not only as a possibility but as a necessity. The first model experiments appear to be promising because of prebiotic-type synthesis by means of transition-metal complexes. It is especially significant that in some instances various types of vitally important substances (nucleic bases, amino acids) are formed simultaneously. There is ground to hope that systematic studies in this field will clarify the role of transition-metal complexes in the organizatorial phase of chemical evolution. It is obvious that researchers working in the fields of the chemistry of cyano and carbonyl complexes, and of the catalytic effect of transition-metal complexes are best suited to study these aspects of the attractive and interesting problem of the origin of life.

Beck, M.↗
NASA NTRS1980

Formation of complex impact craters - Evidence from Mars and other planets

An analysis of the depth vs diameter data of Arthur (1980), is given along with geomorphic data for 73 Martian craters. The implications for the formation of complex impact craters on solid planets is discussed. The analysis integrates detailed morphological observations on planetary craters with geologic data from terrestrial meteorite and explosion craters. The simple to complex transition for impact craters on Mars appears at diameters in the range of 3 to 8 km. Five features appear sequentially with increasing crater size, flat floors, central peaks and shallower depths, scalloped rims, and terraced walls. This order suggests that a shallow depth of excavation and a rebound mechanism have produced the central peaks, not centripetal collapse and deep sliding. Simple craters are relatively uniform in shape from planet to planet, but complex craters vary considerably. Both the average onset diameter for complex impact craters on Mars and the average depth of complex craters vary inversely with gravitational acceleration on four planets.

Pike, R. J.↗
NASA NTRS1985

Turbulence modelling for complex shear flows

The turbulence models available for the prediction of complex turbulent shear layers are reviewed in this paper, concentrating mainly on three-dimensional flows, flows subjected to curvature and body rotation, separated flows, and vortex flows. A critical review of zero-equation, one-equation, two-equation, algebraic Reynolds stress, and full Reynolds stress models are carried out, with a specific emphasis on their applicability to complex flows. It is concluded that algebraic eddy viscosity models and kappa-epsilon/kappa-omega models, with a constant value of coefficients, are not adequate for complex flows. The models which include a description of stresses, either through an algebraic Reynolds stress model or a full Reynolds stress model, are essential for adequate prediction of these flows. It is recommended that systematic experimental investigations be carried out to isolate various complex interactions in order to understand and model the various effects and to carry out an extension of the present models to include complex flows.

Lakshminarayana, B.↗
NASA NTRS1990

Infrared spectra of van de Waals complexes of importance in planetary atmospheres

It has been suggested that (CO2)2 and Ar-CO2 are important constituents of the planetary atmospheres of Venus and Mars. Recent results on the laboratory spectroscopy of CO2 containing van der Waals complexes which may be of use in the modeling of the spectra of planetary atmospheres are presented. Sub-Doppler infrared spectra were obtained for (CO2)2, (CO2)3, and rare-gas-CO2 complexes in the vicinity of the CO2 Fermi diad at 2.7 micrometers using a color-center-laser optothermal spectrometer. From the spectroscopic constants the geometries of the complexes have been determined and van der Waals vibrational frequencies have been estimated. The equilibrium configurations are C2h, C3h, and C2v, for (CO2)2, (CO2)3, and the rare-gas-CO2 complexes, respectively. Most of the homogeneous linewidths for the revibrational transitions range from 0.5 to 22 MHz, indicating that predissociation is as much as four orders of magnitude faster than radiative processes for vibrational relaxation in these complexes.

Fraser, G. T.↗
NASA NTRS1989

Altiplano-Puna volcanic complex of the central Andes

A model is presented accounting for many features of the Altiplano-Puna volcanic complex situated in the Central Volcanic Zone of the Andes which contains 50 recently active volcanoes. The dominant elements of the complex are several large nested caldera complexes which are the source structures for the major regionally distributed ignimbrite sheets that characterize the complex. The study of the complex reveals the importance of the intersection of subsidiary axis-oblique tectonic trends related to regional stress fields peculiar to individual oceanic ridge sections with the axis-parallel trends predominant at all spreading centers in localizing hydrothermal discharge zones.

De Silva, S. L.↗
NASA NTRS1990

On complexity of trellis structure of linear block codes

The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.

Lin, Shu↗