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DOE OSTI2022

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2018

The Utilization Profiles of the CCSDS Unified Space Link Protocol (USLP)

The purpose of this paper is to identify the utilization profiles for interfacing the Data Protocol Sublayer using the Unified Space Link Protocols (USLP) (reference 1) with the space link coding procedures as specified in the CCSDS Coding & Synchronization Blue Books (references 2 through 5), used in both telecommand and telemetry applications. This paper describes how the USLP Protocol utilizes the coding and synchronization sublayer to support: a. Direct to Earth (DTE) telemetry links for engineering and science data b. Direct to Earth (DTE) telemetry links for very high rate science data c. Direct from Earth (DFE) command, sequencing and flight software loads d. Space to Space Links (Proximity) utilized by orbiters for data exchange to/from surface bound assets. The CCSDS has divided the functions of the Data Link Layer into two sublayers: the Data Link Protocol Sublayer (DLP-SL) and the Coding and Synchronization Sublayer (CS-SL). The Data Link Protocol Sublayer (DLP-SL) interfaces to the users, accepting the data that is to be transported, on the sending side of the link, and delivering that data on the receiving end. The Transfer Frame is the data unit that is transferred across the Data Link Protocol Sublayer and the Coding and Synchronization Sublayer boundary. The Coding and Synchronization Sublayer (CS-SL) provides the encoding, randomization, and frame synchronization functions that prepares the USLP Transfer Frame for transport across the space link. The CS-SL is divided into 2 processes: 1) The Frame Interface Processes (FIP) performs the interface functions required to prepare the data for delivery to the Coding/Decoding Process (CDP). This process includes prepending a Frame Start Marker to the provided frame, when management has designated that the frame is not to be aligned to the codeblock or when there is no block code used. 2) The Coding/Decoding Process (CDP) performs the forward error correction processes that are used to optimize the performance of the link and minimize the error rate. The CDP creates the symbol stream that is delivered to the Physical Layer. The transfer of the USLP transfer frames across different types of space links is the focus of this paper. The Protocol Data Unit (PDU) that is passed in both directions between the Data Link Protocol Sublayer (DLP-SL) and Coding and Synchronization Sublayer (CS-SL) is the transfer frame. The USLP frame structure provides flexibility that can be constrained by the functions utilized within the CS-SL that prepare the transfer frame for transit. For example, the USLP transfer frame contains a length field that enables the frame to be of variable length but CS-SL under certain conditions may constrain the frame to be fixed in length. This paper describes 5 operational modes available for use by the Data Link Layer to provide data exchange across the USLP space link. These modes are different because different operational requirements apply to vastly different types of space links and thus the communications implementation requirements differ. The environmental issues include the power or energy available, the distance between the end points of the link, the complexity of the equipment available at those end points, the atmospheric conditions and radiometric frequency selection. The CS-SL utilizes different forward error correcting codes supported by specific operational modes to configure the data for transit. This paper describes all of the operational modes in a series of data models which decompose the functionality between the Data Link Protocol Sublayer and the Coding and Synchronization sublayer. The operational modes described are: 1. Uncoded Mode: has been used for short links that contain significant available power to provide an acceptable frame error rate. The frames in this mode can be variable in length and typically use an error detection algorithm (i.e., CRC) to determine if there are errors in the received frame. 2. Convolutional Only Mode: is currently the prime forward error correction coding used for the proximity links. The frames in this mode can be variable in length and typically use an error detection algorithm (i.e., CRC) to determine if there are errors in the received frame. 3. Variable Length Frame Aligned to Variable Length Codeblock (TC): is used for Direct from Earth links were power levels are high and the simple, least complex code i.e., the BCH code is used. This mode has been in use since the early 1970s. The BCH code is a short code and the decoder is easy to implement. 4. Fixed Length Frame Aligned to Fixed Length Codeblock (AOS/TM): was introduced when the concatenated Convolutional and Reed-Solomon Code was formulated to provide significant reduction in link data error rate and the ability to determine if there was an error in the decoded codeblock. The frame is aligned to the codeblock so that there is a one to one relationship of frame errors to codeblock errors without additional error detection coding being added. This mode requires the protocol frames to be the exact size of the message portion of the codeblock. 5. Frames Unaligned to Fixed Length Codeblocks (Currently used for very high rates and space to space links): This mode is currently used for missions that have a very high data rate that can be controlled adaptively as the environment changes and as the next generation operating mode for the proximity link. This mode from a coded data stream point of view is exactly like that described in 4. above, except that the frame need not be aligned to the codeblock. There is no requirement on frame length when using this mode. Thus when using USLP it can be used to support links that require short or long frames. There is also no mandatory requirement that frames cannot be separated by idle data reducing the tight data rate connection requirements between the data link protocol sublayer and the coding & synchronization sublayer. In conclusion, how these operational modes can be put to use in mission operational scenarios is described for Direct from Earth links (DFE), Direct to Earth links (DTE), and Proximity links.

Greenberg, E.↗

DOE OSTI2026

Hierarchical Chiral Self-Assembly of Nanocylinders Composed of Sequence-Defined Mesogenic Dimers

Chiral ensembles can arise through supramolecular curvature that resolves geometric frustrations in the packing of bent, achiral molecular or colloidal building blocks. Here, we leverage orthogonal protection−deprotection click chemistry to create sequence-defined mesogenic heterodimers exhibiting emergent chirality. We compare the hierarchical self-assembly of the synthesized asymmetric, achiral heterodimers, which differ only in the position of a methyl substituent. Both dimers form chiral spherulites composed of nanocylinders. However, the detailed arrangement of nanocylinders depends on the position of the methyl substituent and the crystallization conditions. Despite the chemical similarity, in one dimer, two crystalline forms are optically active. They form conglomerates of dextrorotatory and levorotatory spherulites. The other dimer forms more highly anisotropic spherulites that mask circular birefringence arising from the misorientation of nanocylinders, while mapping of nanocylinder directors reveals a sense at the spherulite surface. We propose that differences in nanocylinder arrangements may arise from changes in nanocylinder curvature and dimensions dictated by the methyl substituent position, inducing chirality. These results demonstrate multiscale hierarchical assembly relevant to dense systems of tubular structures and highlight the role of sequence and molecular design in directing the bottom-up hierarchical self-assembly and chirality of mesogenic systems.

Alkyls↗

DOE OSTI2025

Sequential Stress Identifies Processing Defects in Bifacial Photovoltaic Modules That Limit Durability

Here, we use sequential stress to investigate hurdles to bifacial photovoltaic (PV) module durability from lamination defects. We test mini-modules with glass/glass (G/G) and glass/transparent-backsheet (G/TB) constructions using either ethylene vinyl acetate or polyolefin elastomer (POE) based encapsulants under a modified IEC 63209-2 sequential stress. This sequence includes multiple iterations of damp heat (DH200), full spectrum light exposure (A3), thermal cycling (TC50), and humidity/freeze (HF10). We compare indoor stress with outdoor exposure. Results show similar relative trends in degradation after a year outdoors compared to our first stress cycle. Subsequent stress cycles impart more severe damage than outdoor exposure for the short outdoor duration used here. Edge-pinch lamination defects in G/G mini-modules limit durability causing delamination and cell cracks. Conversely, we observe greater degradation in G/TB mini-modules compared to G/G in the later stages of the stress sequence when the backsheets are directly exposed to UV-containing light. Our results highlight: 1) the utility of sequential stress testing to uncover degradation modes in bifacial PV, 2) implications of using mini-modules for testing PV quality, and 3) the importance of lamination defects that must be avoided to ensure durability as the industry adopts G/G or G/TB packaging.

14 SOLAR ENERGY↗

DOE OSTI2025

A multifunctional sesquiterpene synthase integrates with cytochrome P450s to reinforce the terpenoid defense network in maize

Terpenoids, the largest and most structurally diverse class of plant natural products, play essential roles in maize defense and ecological interactions. In this study, we identified and functionally characterized a sesquiterpenoid-based defense pathway in maize centered on α-santalenoic acid, a pathogen-inducible sesquiterpenoid antibiotic. Using a combination of metabolite-based genome-wide association studies (mGWAS), linkage mapping, and heterologous expression assays, we identified ZmTPS9 as a multiproduct terpene synthase that primarily produces α-santalene and β-bisabolene. Sequence analysis and site-directed mutagenesis revealed that threonine at position 413 is critical for enzyme activity, with its deletion resulting in a complete loss of enzyme activity. The sesquiterpene hydrocarbons produced by ZmTPS9 are further oxidized by three cytochrome P450 monooxygenases, ZmCYP71Z16, ZmCYP71Z18, and ZmCYP71Z19, to yield antimicrobial metabolites including α-santalenoic acid, zealexin D1 (ZD1), and zealexin D2 (ZD2). Together, these findings demonstrate a convergent biosynthetic strategy in maize, where multiproduct terpene synthases and promiscuous P450s collaboratively generate a flexible and robust terpenoid defense network.

a-santalenoic acid↗

DOE OSTI2023

EvoProtGrad (Directed Evolution for Proteins with Gradients) [SWR-23-48]

A Python package for directed evolution on a protein sequence with gradient-based discrete Markov chain monte carlo (MCMC). Users are able to compose custom models that map sequence to function with pretrained models, including protein language models (PLMs), to guide and constrain search. Our package natively integrates with the HuggingFace platform and supports PLMs from transformers. Our MCMC sampler identifies promising amino acids to mutate via model gradients taken with respect to the input (i.e., sensitivity analysis). We allow users to compose their own custom target function for MCMC by leveraging the Product of Experts MCMC paradigm. Each model is an "expert" that contributes its own knowledge about the protein's fitness landscape to the overall target function. The sampler is designed to be more efficient and effective than brute force and random search while maintaining most of the generality and flexibility. Additional information can be found in the related publication: https://iopscience.iop.org/article/10.1088/2632-2153/accacd

Emami, Patrick↗

DOE OSTI2022

Quantification of Sub-Pixel Dynamics in High-Speed Neutron Imaging

The high penetration depth of neutrons through many metals and other common materials makes neutron imaging an attractive method for non-destructively probing the internal structure and dynamics of objects or systems that may not be accessible by conventional means, such as X-ray or optical imaging. While neutron imaging has been demonstrated to achieve a spatial resolution below 10 μm and temporal resolution below 10 μs, the relatively low flux of neutron sources and the limitations of existing neutron detectors have, until now, dictated that these cannot be achieved simultaneously, which substantially restricts the applicability of neutron imaging to many fields of research that could otherwise benefit from its unique capabilities. In this work, we present an attenuation modeling approach to the quantification of sub-pixel dynamics in cyclic ensemble neutron image sequences of an automotive gasoline direct injector at a 5 μs time scale with a spatial noise floor in the order of 5 μm.

47 OTHER INSTRUMENTATION↗

NASA NTRS1970

An improved conjugate direction minimization procedure

Conjugate direction minimization procedure based on sequences and inferred second partial derivative matrix inverse

Johnson, I. L., Jr.↗

NASA NTRS1973

A geometric theory for the QR, LU and power iterations.

Consideration of the task of computing the invariant subspaces of a given matrix. For this purpose the LU, QR, treppen and bi-iterations have been presented, used, and studied more or less independently of the old-fashioned power method. Each of these methods generates implicitly a sequence of subspaces which determines the convergence properties of the method. The iterations differ in the way in which a basis is constructed to represent each subspace. This aspect largely determines the usefulness of the method. It is shown that the first four iterations produce exactly the same sequence of subspaces as do direct and inverse iteration started from appropriate subspaces. Their convergence properties are therefore the same, and a complete geometric convergence theory is presented in terms of the power method. It is shown that Hessenberg matrices are associated with ideal starting spaces.

Parlett, B. N.↗

NASA NTRS1979

Biomedical ultrasonoscope

The combination of a "C" mode scan electronics in a portable, battery powered biomedical ultrasonoscope having "A" and "M" mode scan electronics, the latter including a clock generator for generating clock pulses, a cathode ray tube having X, Y and Z axis inputs, a sweep generator connected between the clock generator and the X axis input of the cathode ray tube for generating a cathode ray sweep signal synchronized by the clock pulses, and a receiver adapted to be connected to the Z axis input of the cathode ray tube. The "C" mode scan electronics comprises a plurality of transducer elements arranged in a row and adapted to be positioned on the skin of the patient's body for converting a pulsed electrical signal to a pulsed ultrasonic signal, radiating the ultrasonic signal into the patient's body, picking up the echoes reflected from interfaces in the patient's body and converting the echoes to electrical signals; a plurality of transmitters, each transmitter being coupled to a respective transducer for transmitting a pulsed electrical signal thereto and for transmitting the converted electrical echo signals directly to the receiver, a sequencer connected between the clock generator and the plurality of transmitters and responsive to the clock pulses for firing the transmitters in cyclic order; and a staircase voltage generator connected between the clock generator and the Y axis input of the cathode ray tube for generating a staircase voltage having steps synchronized by the clock pulses.

Lee, R. D.↗

NASA NTRS1984

Dynamic stress analysis of smooth and notched fiber composite flexural specimens

A detailed analysis of the dynamic stress field in smooth and notched fiber composite (Charpy-type) specimens is reported in this paper. The analysis is performed with the aid of the direct transient response analysis solution sequence of MSC/NASTRAN. Three unidirectional composites were chosen for the study. They are S-Glass/Epoxy, Kevlar/Epoxy and T-300/Epoxy composite systems. The specimens are subjected to an impact load which is modeled as a triangular impulse with a maximum of 2000 lb and a duration of 1 ms. The results are compared with those of static analysis of the specimens subjected to a peak load of 2000 lb. For the geometry and type of materials studied, the static analysis results gave close conservative estimates for the dynamic stresses. Another interesting inference from the study is that the impact induced effects are felt by S-Glass/Epoxy specimens sooner than Kevlar/Epoxy or T-300/Epoxy specimens.

Murthy, P. L. N.↗

NASA NTRS1986

Dynamic stress analysis of smooth and notched fiber composite flexural specimens

Murthy, P. L. N.↗

NASA NTRS1991

NASTRAN GPWG tables for combined substructures

A method for computing the mass and center of gravity for basic and combined substructures stored in the NASTRAN Substructure Operating File (SOF) is described. The three step method recovers SOF data blocks for the relevant substructure, processes these data blocks using a specially developed FORTRAN routine, and generates the NASTRAN gridpoint weight generator (GPWG) table for the substructure in a PHASE2 SOF execution using a Direct Matrix Abstraction Program (DMAP) sequence. Verification data for the process is also provided.

Allen, Tom↗

NASA NTRS1992

Artificial intelligence approach to planning the robotic assembly of large tetrahedral truss structures

An assembly planner for tetrahedral truss structures is presented. To overcome the difficulties due to the large number of parts, the planner exploits the simplicity and uniformity of the shapes of the parts and the regularity of their interconnection. The planning automation is based on the computational formalism known as production system. The global data base consists of a hexagonal grid representation of the truss structure. This representation captures the regularity of tetrahedral truss structures and their multiple hierarchies. It maps into quadratic grids and can be implemented in a computer by using a two-dimensional array data structure. By maintaining the multiple hierarchies explicitly in the model, the choice of a particular hierarchy is only made when needed, thus allowing a more informed decision. Furthermore, testing the preconditions of the production rules is simple because the patterned way in which the struts are interconnected is incorporated into the topology of the hexagonal grid. A directed graph representation of assembly sequences allows the use of both graph search and backtracking control strategies.

Homemdemello, Luiz S.↗

NASA NTRS1999

Adaptive Error Estimation in Linearized Ocean General Circulation Models

Data assimilation methods are routinely used in oceanography. The statistics of the model and measurement errors need to be specified a priori. This study addresses the problem of estimating model and measurement error statistics from observations. We start by testing innovation based methods of adaptive error estimation with low-dimensional models in the North Pacific (5-60 deg N, 132-252 deg E) to TOPEX/POSEIDON (TIP) sea level anomaly data, acoustic tomography data from the ATOC project, and the MIT General Circulation Model (GCM). A reduced state linear model that describes large scale internal (baroclinic) error dynamics is used. The methods are shown to be sensitive to the initial guess for the error statistics and the type of observations. A new off-line approach is developed, the covariance matching approach (CMA), where covariance matrices of model-data residuals are "matched" to their theoretical expectations using familiar least squares methods. This method uses observations directly instead of the innovations sequence and is shown to be related to the MT method and the method of Fu et al. (1993). Twin experiments using the same linearized MIT GCM suggest that altimetric data are ill-suited to the estimation of internal GCM errors, but that such estimates can in theory be obtained using acoustic data. The CMA is then applied to T/P sea level anomaly data and a linearization of a global GFDL GCM which uses two vertical modes. We show that the CMA method can be used with a global model and a global data set, and that the estimates of the error statistics are robust. We show that the fraction of the GCM-T/P residual variance explained by the model error is larger than that derived in Fukumori et al.(1999) with the method of Fu et al.(1993). Most of the model error is explained by the barotropic mode. However, we find that impact of the change in the error statistics on the data assimilation estimates is very small. This is explained by the large representation error, i.e. the dominance of the mesoscale eddies in the T/P signal, which are not part of the 21 by 1" GCM. Therefore, the impact of the observations on the assimilation is very small even after the adjustment of the error statistics. This work demonstrates that simult&neous estimation of the model and measurement error statistics for data assimilation with global ocean data sets and linearized GCMs is possible. However, the error covariance estimation problem is in general highly underdetermined, much more so than the state estimation problem. In other words there exist a very large number of statistical models that can be made consistent with the available data. Therefore, methods for obtaining quantitative error estimates, powerful though they may be, cannot replace physical insight. Used in the right context, as a tool for guiding the choice of a small number of model error parameters, covariance matching can be a useful addition to the repertory of tools available to oceanographers.

Chechelnitsky, Michael Y.↗

NASA NTRS2002

A genomic regulatory network for development

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

Non-NASA Center↗

NASA NTRS2010

Study of the Microbial Diversity of a Newly Discovered East Antarctic Freshwater Lake, L27C, and of a Perennially Ice-Covered Lake Untersee

The microbial communities that reside within freshwater lakes of Schirmacher and Untersee Oases in East Antarctica must cope with extreme conditions that may include cold temperature, annual freeze-thaw cycles, exposure to UV radiation, especially during the austral summer months, low light beneath thick ice-cover, followed by seasonal darkness. The objective of this study was to assess the microbial biodiversity and distribution from samples taken from two freshwater lakes (L27C and Lake Untersee) that were collected during the Tawani 2008 International Antarctic Expedition that conducted research in this region of Antarctica. L27C is a small, previously unreported lake residing 2 km WNW of Maitri Station at Schirmacher Oasis. Biodiversity and distribution of microorganisms within the lake were studied using both culture-independent and culture-dependent methodologies based upon the analysis of eubacterial 16S rRNA gene sequences. Lake Untersee, a perennially ice-covered, ultra-oligotrophic, lake in the Otto-von-Gruber-Gebirge (Gruber Mountains) of central Dronning Maud Land was also sampled and the microbial diversity was analyzed by eubacterial 16S rRNA gene sequences derived from pure cultures. Direct culturing of water samples from each lake on separate R2A growth medium exhibited a variety of microorganisms including: Janthinobacterium, Hymenobacter, Sphingamonas, Subtercola, Deinococcus, Arthrobacter, Flavobacterium, Polaromonas, Rhodoferax and Duganella. The evaluation of samples from L27C through culture-independent methodology identified a rich microbial diversity consisting of six different phyla of bacteria. The culture-independent analysis also displayed the majority of bacteria (56%) belonged to the Class gamma-proteobacteria within the phylum Proteobacteria. Within the Class gamma-proteobacteria, Acinetobacter dominated (48%) the total microbial load. Overall, L27C exhibited 7 different phyla of bacteria and 20 different genera. Statistical analysis (Shannon-Weaver Diversity Index and Simpson Diversity Index) of the biodiversity of L27C displayed a moderately rich and diverse community. Investigations of the biodiversity and distribution of microorganisms in these lakes will help further our understanding of how the physical environment impact the structure and function within these microbially dominated ecosystems.

Huang, Jonathan P.↗

NASA NTRS2009

Observations of Screw Dislocation Driven Growth and Faceting During CVD Homoepitaxy on 4H-SiC On-Axis Mesa Arrays

Previous studies of (0001) homoepitaxial growth carried out on arrays of small-area mesas etched into on-axis silicon-face 4H-SiC wafers have demonstrated that spiral growth emanating from at least one screw dislocation threading the mesa is necessary in order for a mesa to grow taller in the <0001> (c-axis vertical) direction while maintaining 4H stacking sequence [1]. However, even amongst mesas containing the screw dislocation step source necessary for vertical c-axis growth, we have observed striking differences in the height and faceting that evolve during prolonged homoepitaxial growths. This paper summarizes Atomic Force Microscopy (AFM), Electron Channeling Contrast Imaging (ECCI), Scanning Electron Microscopy (SEM), and optical microscopy observations of this phenomenon. These observations support our initially proposed model [2] that the observed large variation (for mesas where 3C-SiC nucleation has not occurred) is related to the lateral positioning of a screw dislocation step source within each etched mesa. When the screw dislocation step source is located close enough to the developing edge/sidewall facet of a mesa, the c-axis growth rate and facet angle are affected by the resulting interaction. In particular, the intersection (or near intersection) of the inward-sloping mesa sidewall facet with the screw dislocation appears to impede the rate at which the spiral provides new steps required for c-axis growth. Also, the inward slope of the sidewall facet during growth (relative to other sidewalls of the same mesa not near the screw dislocation) seems to be impeded by the screw dislocation. In contrast, mesas whose screw dislocations are centrally located grow vertically, but inward sloping sidewall facets shrink the area of the top (0001) growth surface almost to the point of vanishing.

Neudeck, Philip G.↗