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At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
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 OSTI2016

THE FIRST DISTANCE CONSTRAINT ON THE RENEGADE HIGH-VELOCITY CLOUD COMPLEX WD

We present medium-resolution, near-ultraviolet Very Large Telescope/FLAMES observations of the star USNO-A0600-15865535. We adapt a standard method of stellar typing to our measurement of the shape of the Balmer ϵ absorption line to demonstrate that USNO-A0600-15865535 is a blue horizontal branch star, residing in the lower stellar halo at a distance of 4.4 kpc from the Sun. We measure the H and K lines of singly ionized calcium and find two isolated velocity components, one originating in the disk, and one associated with the high-velocity cloud complex WD. This detection demonstrated that complex WD is closer than ∼4.4 kpc and is the first distance constraint on the +100 km s{sup −1} Galactic complex of clouds. We find that complex WD is not in corotation with the Galactic disk, which has been assumed for decades. We examine a number of scenarios and find that the most likely scenario is that complex WD was ejected from the solar neighborhood and is only a few kiloparsecs from the Sun.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Characterizing wind gusts in complex terrain

Abstract. Wind gusts are a key driver of aerodynamic loading, especially for tall structures such a bridges and wind turbines. However, gust characteristics in complex terrain are not well understood and common approximations used to describe wind gust behavior may not be appropriate at heights relevant to wind turbines and other structures. Data collected in the Perdigão experiment are analyzed herein to provide a foundation for improved wind gust characterization and process-level understanding of flow intermittency in complex terrain. High-resolution observations from sonic anemometers and vertically pointing Doppler lidars are used to conduct a detailed study of gust characteristics with a specific focus on the parent distributions of nine gust parameters (that describe velocity, time, and length scales), their joint distributions, height variation, and coherence in the vertical and horizontal planes. Best-fit distributional forms for varying gust properties show good agreement with those from previous experiments in moderately complex terrain but generate nonconservative estimates of the gust properties that are of key importance to structural loading. Probability distributions of gust magnitude derived from vertically pointing Doppler lidars exhibit good agreement with estimates from sonic anemometers despite differences arising from volumetric averaging and the terrain complexity. Wind speed coherence functions during gusty periods (which are important to structural wind loading) are similar to less complex sites for small vertical displacements (10 to 40 m), but do not exhibit an exponential form for larger horizontal displacements (800 to 1500 m).

Letson, Frederick (ORCID:0000000192750359)↗
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.↗
DOE OSTI2017

Structure of the active form of human origin recognition complex and its ATPase motor module

Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations.

Tocilj, Ante↗
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↗
NASA NTRS1991

The physical properties of giant molecular cloud complexes in the outer Galaxy - Implications for the ratio of H2 column density to (C-12)O intensity

The physical properties of 35 giant molecular cloud complexes in the outer Galaxy were derived from the Goddard-Columbia surveys of the Galactic plane region (Dame et al., 1987). The spatial and radial velocity boundaries for the individual cloud complexes were estimated by analyzing the spatial and velocity structure of emission features in the (C-12)O surveys, and the distance to each cmplex was determined kinematically on the assumption of a flat rotation curve. The ratio of the H2 column density to the (C-12)O intensity for the outer Galaxy complexes was found to be about 6.0 x 10 to the 20th molecules/sq cm K per km/sec, which is by a factor of 2-3 greater than the value derived by other auhtors for the inner Galaxy complexes. This increase in the H2 column density/(C-12)O intensity with the distance from with the Galactic center is consistent with predictions of the optically thick cloudlet model of giant molecular cloud complexes.

Sodroski, T. J.↗