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Results for “Complexity bounding”

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.

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS2010

Model-Checking with Edge-Valued Decision Diagrams

We describe an algebra of Edge-Valued Decision Diagrams (EVMDDs) to encode arithmetic functions and its implementation in a model checking library along with state-of-the-art algorithms for building the transition relation and the state space of discrete state systems. We provide efficient algorithms for manipulating EVMDDs and give upper bounds of the theoretical time complexity of these algorithms for all basic arithmetic and relational operators. We also demonstrate that the time complexity of the generic recursive algorithm for applying a binary operator on EVMDDs is no worse than that of Multi-Terminal Decision Diagrams. We have implemented a new symbolic model checker with the intention to represent in one formalism the best techniques available at the moment across a spectrum of existing tools: EVMDDs for encoding arithmetic expressions, identity-reduced MDDs for representing the transition relation, and the saturation algorithm for reachability analysis. We compare our new symbolic model checking EVMDD library with the widely used CUDD package and show that, in many cases, our tool is several orders of magnitude faster than CUDD.

Roux, Pierre↗
DOE OSTI2020

Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Gαi1

Abstract Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Gα) and serves as an essential Gα chaperone. Mechanisms by which Ric-8A catalyzes these activities, which are stimulated by Casein Kinase II phosphorylation, are unknown. We report the structure of the nanobody-stabilized complex of nucleotide-free Gα bound to phosphorylated Ric-8A at near atomic resolution by cryo-electron microscopy and X-ray crystallography. The mechanism of Ric-8A GEF activity differs considerably from that employed by G protein-coupled receptors at the plasma membrane. Ric-8A engages a specific conformation of Gα at multiple interfaces to form a complex that is stabilized by phosphorylation within a Ric-8A segment that connects two Gα binding sites. The C-terminus of Gα is ejected from its beta sheet core, thereby dismantling the GDP binding site. Ric-8A binds to the exposed Gα beta sheet and switch II to stabilize the nucleotide-free state of Gα.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantum error correction from complexity in Brownian SYK

We study the robustness of quantum error correction in a one-parameter ensemble of codes generated by the Brownian SYK model, where the parameter quantifies the encoding complexity. The robustness of error correction by a quantum code is upper bounded by the “mutual purity” of a certain entangled state between the code subspace and environment in the isometric extension of the error channel, where the mutual purity of a density matrix ρAB is the difference $\mathcal{F}$ p ($A : B$) ≡ $\mathrm{T}$r $p^{2}_{AB}$ - $\mathrm{T}$r $p^{2}_{A}$ $\mathrm{T}$r $p^{2}_{B}$. We show that when the encoding complexity is small, the mutual purity is O(1) for the erasure of a small number of qubits (i.e., the encoding is fragile). However, this quantity decays exponentially, becoming O(1/N) for O(log N) encoding complexity. Further, at polynomial encoding complexity, the mutual purity saturates to a plateau of O(e -N ). We also find a hierarchy of complexity scales associated to a tower of subleading contributions to the mutual purity that quantitatively, but not qualitatively, adjust our error correction bound as encoding complexity increases. In the AdS/CFT context, our results suggest that any portion of the entanglement wedge of a general boundary subregion A with sufficiently high encoding complexity is robustly protected against low-rank errors acting on A with no prior access to the encoding map. From the bulk point of view, we expect such bulk degrees of freedom to be causally inaccessible from the region A despite being encoded in it.

1/N expansion↗
DOE OSTI2026

Quantum Time-Space Tradeoffs for Matrix Problems

We consider the time and space required for quantum computers to solve a wide variety of problems involving matrices, many of which have only been analyzed classically in prior work. Our main results show that for a range of linear algebra problems—including matrix-vector product, matrix inversion, matrix multiplication and powering—existing classical time-space tradeoffs, several of which are tight for every space bound, also apply to quantum algorithms with at most a constant factor loss. For example, for almost all fixed matrices 𝐴, including the discrete Fourier transform matrix, we prove that quantum circuits with at most 𝑇 input queries and 𝑆 qubits of memory require 𝑇 = Ω⁢(𝑛 2 /𝑆) to compute matrix-vector product 𝐴⁢𝑥 for 𝑥 ∈{0,1 𝑛 . We similarly prove that matrix multiplication for 𝑛 ×𝑛 binary matrices requires 𝑇 = Ω⁢(𝑛 3 /$\sqrt{𝑆}$). Because many of our lower bounds are matched by deterministic algorithms with the same time and space complexity, our results show that quantum computers cannot provide any asymptotic advantage for these problems with any space bound. We obtain matching lower bounds for the stronger notion of quantum cumulative memory complexity—the sum of the space per layer of a circuit. We also consider Boolean (i.e., AND-OR) matrix multiplication and matrix-vector products, improving the previous quantum time-space tradeoff lower bounds for 𝑛 × 𝑛 Boolean matrix multiplication to 𝑇 = Ω⁢(𝑛 2.5 /𝑆 1/4 ) from 𝑇 = Ω⁢(𝑛 2.5 /𝑆 1/2 ). Our improved lower bound for Boolean matrix multiplication is based on a new coloring argument that extracts more from the strong direct product theorem that was the basis for prior work. To obtain our tight lower bounds for linear algebra problems, we require much stronger bounds than strong direct product theorems. We obtain these bounds by adding a new bucketing method to the quantum recording-query technique of Zhandry that lets us apply classical arguments to upper bound the success probability of quantum circuits.

lower bounds↗
DOE OSTI2021

Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex

The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA + ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3–REV7 binary and fused SHLD2–SHLD3–REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2–SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2–SHLD3–REV7–TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Revisiting Theoretical Limits for One Degree-of-Freedom Wave Energy Converters

This work revisits the theoretical limits of one degree-of-freedom wave energy converters (WECs). This work considers the floating sphere used in the OES Task 10 WEC modeling and verification effort for analysis. Analytical equations are derived to determine bounds on displacement amplitude, time-averaged power (TAP), and power-take-off (PTO) force. A unique result found shows that the TAP absorbed by a WEC can be defined solely by the inertial properties and radiation hydrodynamic coefficients. In addition, a unique expression for the PTO force was derived that provides lower and upper bounds when resistive control is used to maximize power generation. For complex conjugate control, this same expression only provides a lower bound, as there is theoretically no upper bound. These bounds assist in comparing the performance of the floating sphere if it were to extract energy using surge or heave motion. The analysis shows because of differences in hydrodynamic coefficients for each oscillating mode, there are different frequency ranges that provide better power capture efficiency. The influence of a motion constraint on TAP while utilizing a nonideal power take-off is examined and found to reduce the losses associated with bidirectional energy flow. The expression to calculate TAP with a nonideal PTO is modified by the electrical conversion efficiency and the ratio of the PTO spring and damping coefficients. Furthermore, the PTO spring and damping coefficients were separated in the expression, allowing for limits to be set on the PTO coefficients to ensure net power generation.

16 TIDAL AND WAVE POWER↗
DOE OSTI2025

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.

Jaiswal, Rahul↗
NASA NTRS1995

Kinematics and dynamics of the MKW/AWM poor clusters

We report 472 new redshifts for 416 galaxies in the regions of the 23 poor clusters of galaxies originally identified by Morgan, Kayser, and White (MKW), and Albert, White, and Morgan (AWM). Eighteen of the poor clusters now have 10 or more available redshifts within 1.5/h Mpc of the central galaxy; 11 clusters have at least 20 available redshifts. Based on the 21 clusters for which we have sufficient velocity information, the median velocity scale is 336 km/s, a factor of 2 smaller than found for rich clusters. Several of the poor clusters exhibit complex velocity distributions due to the presence of nearby clumps of galaxies. We check on the velocity of the dominant galaxy in each poor cluster relative to the remaining cluster members. Significantly high relative velocities of the dominant galaxy are found in only 4 of 21 poor clusters, 3 of which we suspect are due to contamination of the parent velocity distribution. Several statistical tests indicate that the D/cD galaxies are at the kinematic centers of the parent poor cluster velocity distributions. Mass-to-light ratios for 13 of the 15 poor clusters for which we have the required data are in the range 50 less than or = M/L(sub B(0)) less than or = 200 solar mass/solar luminosity. The complex nature of the regions surrounding many of the poor clusters suggests that these groupings may represent an early epoch of cluster formation. For example, the poor clusters MKW7 and MKWS are shown to be gravitationally bound and likely to merge to form a richer cluster within the next several Gyrs. Eight of the nine other poor clusters for which simple two-body dynamical models can be carried out are consistent with being bound to other clumps in their vicinity. Additional complex systems with more than two gravitationally bound clumps are observed among the poor clusters.

Beers, Timothy C.↗
DOE OSTI2025

Toward scalable bound-to-resonance extrapolations for few- and many-body systems

In open quantum many-body systems, the theoretical description of resonant states of many particles strongly coupled to the continuum can be challenging. Such states are commonplace in, for example, exotic nuclei and hadrons, and can reveal important information about the underlying forces at play in these systems. In this work, we demonstrate that the complex-augmented eigenvector continuation (CA-EC) method, originally formulated for the two-body problem with uniform complex scaling, can reliably perform bound-to-resonance extrapolations for genuine three-body resonances having no bound subsystems. Here, we first establish that three-body bound-to-resonance extrapolations are possible by benchmarking different few-body approaches, and we provide arguments to explain how the extrapolation works in the many-body case. We furthermore pave the way towards scalable resonance extrapolations in many-body systems by showing that the CA-EC method also works in the Berggren basis, studying a realistic application using the Gamow shell model.

Ab initio calculations↗
NASA NTRS1997

Robot Position Sensor Fault Tolerance

Robot systems in critical applications, such as those in space and nuclear environments, must be able to operate during component failure to complete important tasks. One failure mode that has received little attention is the failure of joint position sensors. Current fault tolerant designs require the addition of directly redundant position sensors which can affect joint design. A new method is proposed that utilizes analytical redundancy to allow for continued operation during joint position sensor failure. Joint torque sensors are used with a virtual passive torque controller to make the robot joint stable without position feedback and improve position tracking performance in the presence of unknown link dynamics and end-effector loading. Two Cartesian accelerometer based methods are proposed to determine the position of the joint. The joint specific position determination method utilizes two triaxial accelerometers attached to the link driven by the joint with the failed position sensor. The joint specific method is not computationally complex and the position error is bounded. The system wide position determination method utilizes accelerometers distributed on different robot links and the end-effector to determine the position of sets of multiple joints. The system wide method requires fewer accelerometers than the joint specific method to make all joint position sensors fault tolerant but is more computationally complex and has lower convergence properties. Experiments were conducted on a laboratory manipulator. Both position determination methods were shown to track the actual position satisfactorily. A controller using the position determination methods and the virtual passive torque controller was able to servo the joints to a desired position during position sensor failure.

Aldridge, Hal A.↗
DOE OSTI2020

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as “membrane-distal” and estimate to comprise ~90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.

KRAS↗
DOE OSTI2026

The HypA and HypB metallochaperones from Methanococcus maripaludis have unique metal-binding properties and a distinct nickel transfer mechanism

[NiFe] hydrogenases are widespread microbial metalloenzymes that catalyze the reversible conversion of hydrogen (H2) to protons and electrons, playing key roles in energy metabolism. The biosynthesis of the NiFe(CN) 2 CO cofactor involves a suite of maturation proteins, including the HypA and HypB nickel metallochaperones. Here, we define the metal-binding properties, nucleotide-dependent behavior, and functional interplay of HypA and HypB from the hydrogenotrophic methanogenic archaeon, Methanococcus maripaludis . Methanogens have multiple essential nickel-dependent enzymes, so they require efficient systems for nickel delivery that remain largely unexplored. Purified M. maripaludis HypA binds zinc or mononuclear iron at the C-terminal metal binding site, the latter of which has not been reported in other HypA proteins and may serve a unique regulatory role in methanogens. The G-protein metallochaperone HypB binds nickel at the G-domain, which stimulates GTPase activity. Size exclusion chromatography experiments reveal that HypA and HypB form complexes in the presence of nickel, and zinc-bound HypA is optimized for nickel transfer from HypB. The identity of the nucleotide bound to HypB (GDP or GTP) alters the oligomeric state of HypA-HypB complexes, supporting a GTPase-mediated nickel delivery pathway. The HypA-HypB 2 complex configuration is enriched and stable in the presence of GDP and nickel, indicating that this complex delivers nickel to the hydrogenase as opposed to HypA alone. Interestingly, affinity purification-mass spectrometry revealed that HypB interacts with several nickel-dependent proteins, suggesting that HypB may play a broader role in nickel homeostasis in M. maripaludis . Together, this work establishes a biochemical framework for HypAB-mediated nickel trafficking in methanogens.

[NiFe] hydrogenase↗
DOE OSTI2020

Revisiting Theoretical Limits for One-Degree-of-Freedom Wave Energy Converters

This work revisits the theoretical limits of one-degree-of-freedom wave energy converters. This paper considers the floating sphere used in the Ocean Energy Systems Task 10 Wave Energy Converter modeling and verification effort for analysis. Analytical equations are derived to determine bounds on the motion amplitude, time-averaged power, and power-take-off (PTO) force. A unique result was found that shows the time-averaged power absorbed by a wave energy converter can be defined solely by the inertial properties and radiation hydrodynamic coefficients. In addition, a unique expression for the PTO force amplitude was derived that has provided upper and lower bounds when resistive control is used to maximize power generation. For complex conjugate control, this same expression can only provide a lower bound, as there is theoretically no upper bound. These bounds are used to compare the performance of a floating sphere if it were to extract energy using surge or heave motion. The analysis shows that because of the differences in hydrodynamic coefficients of each oscillating mode, there will be different frequency ranges that provide better power capture efficiency. The influence of a motion constraint on power absorption while also utilizing a nonideal power take-off is examined and found to reduce the losses associated with bidirectional energy flow. The expression to calculate the time-averaged power with a nonideal PTO is modified by the mechanical-to-electrical efficiency and the ratio of the PTO spring and damping coefficients. The PTO spring and damping coefficients were separated in the expression, which allows for limits to be set on the possible values of PTO coefficients to ensure a net flow of power to the grid.

50 EE - Wind and Water Power Program - Water (EE-4↗
DOE OSTI2020

Revisiting Theoretical Limits for One-Degree-of-Freedom Wave Energy Converters: Preprint

This work revisits the theoretical limits of one-degree of freedom wave energy converters (WECs). This paper considers the floating sphere used in the Ocean Energy Systems (OES) Task 10 Wave Energy Converter modeling and verification effort for analysis. Analytical equations are derived to determine bounds on the motion amplitude, time-averaged power, and power take-off (PTO) force. A unique result was found that shows the time-averaged power absorbed by a WEC can be defined solely by the inertial properties and the radiation hydrodynamic coefficients. In addition, a unique expression for the PTO force amplitude was derived which has provided upper and lower bounds when resistive control is used to maximize power generation. For complex conjugate control, this same expression can only provide a lower bound as there is theoretically no upper bound. These bounds are used to compare the performance of a floating sphere if it were to extract energy using surge or heave motion. The analysis shows that because of the differences in hydrodynamic coefficients of each oscillating mode there will be different frequency ranges that provide better power capture efficiency. The influence of a motion constraint on power absorption while also utilizing a nonideal power take-off is examined and found to reduce the losses associated with bidirectional energy flow. The expression to calculate the time-averaged power with a nonideal PTO is modified by the mechanical-to-electrical efficiency and the ratio of the PTO spring and damping coefficients. These were separated in the expression which allows for limits to be set on the possible values of PTO coefficients to ensure a net flow of power to the grid.

50 EE - Wind and Water Power Program - Water (EE-4↗
DOE OSTI2021

Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase

All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hydrated Metal and Metal-Nitrate Complexes in Water: Full Lanthanide(III) Series plus Miscellaneous Metal Ions

This is a dataset of hydrated metal complexes and metal–nitrate hydrated complexes intended for public use, reproducibility, and downstream structural analysis. A key feature is coverage across the full lanthanide(III) series (La–Lu), enabling systematic comparisons of coordination motifs and bonding trends across the entire lanthanide sequence. In addition to the lanthanides, the dataset also includes other metal ions such as UO2(VI), Fe(II), and Fe(III). The dataset provides optimized geometries for hydrated and nitrate-containing hydrated complexes, together with representative ab initio molecular dynamics (AIMD) trajectories saved in standard XYZ formats. The accompanying NWChem input decks enable reproduction of the reported calculations and provide a starting point for extending the simulations to related coordination environments. Computationally, DFT calculations employ the B3LYP functional with DFT-D3BJ dispersion corrections and a COSMO continuum solvent model (dielectric constant 78.4) to represent solvation beyond the explicitly treated first hydration shell. AIMD simulations are performed with the NWChem qmd module at 298 K, integrating nuclear motion with the velocity-Verlet algorithm and controlling temperature using a Nosé–Hoover thermostat. Trajectories are approximately 4.8 ps in length and are used primarily to assess short-time stability of candidate coordination motifs, including (for lanthanides) differences between 8- versus 9-water coordination and comparisons between nitrate-bound and nitrate-free hydrated complexes.

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗
DOE OSTI2021

Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction

The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to biological macromolecules has far-reaching implications for a range of problems, including metabolomics. However, problems such as predicting the bound structure of a protein–ligand complex along with its affinity have proven to be an enormous challenge. In recent years, machine learning-based methods have proven to be more accurate than older methods, many based on simple linear regression. Nonetheless, there remains room for improvement, as these methods are often trained on a small set of features, with a single functional form for any given physical effect, and often with little mention of the rationale behind choosing one functional form over another. Moreover, it is not entirely clear why one machine learning method is favored over another. Here, we endeavor to undertake a comprehensive effort towards developing high-accuracy, machine-learned scoring functions, systematically investigating the effects of machine learning method and choice of features, and, when possible, providing insights into the relevant physics using methods that assess feature importance. Here, we show synergism among disparate features, yielding adjusted R 2 with experimental binding affinities of up to 0.871 on an independent test set and enrichment for native bound structures of up to 0.913. When purely physical terms that model enthalpic and entropic effects are used in the training, we use feature importance assessments to probe the relevant physics and hopefully guide future investigators working on this and other computational chemistry problems.

59 BASIC BIOLOGICAL SCIENCES↗