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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins

Bacteria encode homooligomeric single-stranded (ss) DNA-binding proteins (SSBs) that coat and protect ssDNA intermediates formed during genome maintenance reactions. The prototypical Escherichia coli SSB tetramer can bind ssDNA using multiple modes that differ by the number of bases bound per tetramer and the magnitude of the binding cooperativity. Our understanding of the mechanisms underlying cooperative ssDNA binding by SSBs has been hampered by the limited amount of structural information available for interfaces that link adjacent SSB proteins on ssDNA. Here in this paper we present a crystal structure of Bacillus subtilis SsbA bound to ssDNA. The structure resolves SsbA tetramers joined together by a ssDNA “bridge” and identifies an interface, termed the “bridge interface,” that links adjacent SSB tetramers through an evolutionarily conserved surface near the ssDNA-binding site. E. coli SSB variants with altered bridge interface residues bind ssDNA with reduced cooperativity and with an altered distribution of DNA binding modes. These variants are also more readily displaced from ssDNA by RecA than wild-type SSB. In spite of these biochemical differences, each variant is able to complement deletion of the ssb gene in E. coli. Together our data suggest a model in which the bridge interface contributes to cooperative ssDNA binding and SSB function but that destabilization of the bridge interface is tolerated in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Organic Enrichment at Aqueous Interfaces: Cooperative Adsorption of Glucuronic Acid to DPPC Monolayers Studied with Vibrational Sum Frequency Generation

Surface tension, surface-specific vibrational spectroscopy and differential scanning calorimetry measurements were all used to test cooperative adsorption of glucuronic acid (GU) to DPPC monolayers adsorbed to the aqueous/vapor interface. Experiments were performed using GU solutions prepared in Millipore water and in carbonate/bicarbonate solutions buffered to a pH of 9.0. The effects of GU on DPPC monolayer structure and organization were carried out with tightly packed monolayers (40 Å2/DPPC) and monolayers in their liquid condensed phase (55 Å2/molecule). Surface tension data show that GU concentrations of 50 mM lead to expanded DPPC monolayers with diminished surface tensions (or higher surface pressures) at a given DPPC coverage relative to monolayers on pure water. With unbuffered solutions, GU induces significant ordering within liquid condensed monolayers although the effects of GU on tightly packed DPPC monolayers are less pronounced. GU also induces a second, higher melting temperature in DPPC vesicles implying that GU (at sufficiently high concentrations) strengthens lipid-lipid cohesion, possibly by replacing water solvating the DPPC headgroups. Together, these observations all support a cooperative adsorption mechanism. In buffer solutions, the effects of dissolved GU on DPPC structure and organization are muted. Only at sufficiently high GU concentrations (when the solution’s buffering capacity has been exceeded) do the data again show evidence of cooperative adsorption. These findings place limits on cooperative adsorption’s ability to enrich interfacial organic content in alkaline environmental systems such as oceans.

Link, Katie A.↗
DOE OSTI2025

Combining Theory and Experiment to Map the Atomic-Level Structure–Energy Pathways of Adsorbate-Mediated Phase Changes in a Cooperatively Flexible Metal–Organic Framework

An important subclass of metal–organic frameworks (MOFs) exhibits cooperative flexibility, wherein individual crystallites undergo global structural phase changes in response to external stimuli. Where cooperative flexibility results in reversible changes between crystalline states of distinct accessible porosity, these frameworks can exhibit rare yet desirable behaviors that cannot be explained by local dynamics alone. Yet, the chemical and structural origins of cooperative flexibility and how frameworks undergo these reversible phase changes at the atomic level remain poorly understood. Deliberate design for specific applications is therefore exceedingly difficult, and there is great impetus to develop a fundamental understanding of this phenomenon. Here, an effective and widely accessible computational approach is developed, which is designed to provide microscopic resolution via direct comparison to experimental data along the desorption-guided pathway. The strategy is applied to explain the desorption-induced phase change in an experimentally well-characterized framework, CdIF-13 (sod-Cd(benzimidazolate)2), where experiment alone was unable to resolve the atomistically detailed phase change landscape. Our findings reveal that the cooperative phase change pathways are adsorbate dependent with thermodynamics of intermediate structural states dictated by a nuanced interplay of ligand orientation, skeletal symmetry, and modes of surface adsorption. The results reveal that this isotropically flexible framework is “chaperoned” through a complex energy landscape by specific adsorbates, revealed by the reported computational approach with atomic-level insight and validated by experimentally determined structures. Thus, this work facilitates both understanding and future design of flexible materials for applications in gas storage, transport, delivery, and separation technologies.

03 NATURAL GAS↗
DOE OSTI2018

Cooperative asymmetric reactions combining photocatalysis and enzymatic catalysis

Living organisms rely on simultaneous reactions catalysed by mutually compatible and selective enzymes to synthesize complex natural products and other metabolites. To combine the advantages of these biological systems with the reactivity of artificial chemical catalysts, chemists have devised sequential, concurrent, and cooperative chemoenzymatic reactions that combine enzymatic and artificial catalysts. Cooperative chemoenzymatic reactions consist of interconnected processes that generate products in yields and selectivities that cannot be obtained when the two reactions are carried out sequentially with their respective substrates. However, such reactions are difficult to develop because chemical and enzymatic catalysts generally operate in different media at different temperatures and can deactivate each other. Owing to these constraints, the vast majority of cooperative chemoenzymatic processes that have been reported over the past 30 years can be divided into just two categories: chemoenzymatic dynamic kinetic resolutions of racemic alcohols and amines, and enzymatic reactions requiring the simultaneous regeneration of a cofactor. New approaches to the development of chemoenzymatic reactions are needed to enable valuable chemical transformations beyond this scope. Here in this paper we report a class of cooperative chemoenzymatic reaction that combines photocatalysts that isomerize alkenes with ene-reductases that reduce carbon–carbon double bonds to generate valuable enantioenriched products. This method enables the stereoconvergent reduction of E/Zmixtures of alkenes or reduction of the unreactive stereoisomers of alkenes in yields and enantiomeric excesses that match those obtained from the reduction of the pure, more reactive isomers. The system affords a range of enantioenriched precursors to biologically active compounds. More generally, these results show that the compatibility between photocatalysts and enzymes enables chemoenzymatic processes beyond cofactor regeneration and provides a general strategy for converting stereoselective enzymatic reactions into stereoconvergent ones.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface

In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Concept of Operations of Next-Generation Traffic Control Utilizing Infrastructure-Based Cooperative Perception

This paper provides a system architecture for an infrastructure-based cooperative perception fusion engine for next-generation traffic control. This engine will provide a complete state-space digital representation with measurable accuracy to support a wide-range of applications. The architecture includes inputs, functional flow, data standardization recommendations, outputs, and supported applications. The cooperative perception engine addresses critical needs with respect to accelerating the benefits of automation through intelligent roadway infrastructure, which complements and accelerates connected and automated vehicle (CAV) technology. The cooperative perception acquires and fuses information from sensors (radar, LiDAR, and cameras) and CAVs to perceive roadway traffic states of moving objects, creates a complete 3D digital representation of that state-space, and communicates it to downstream application such as intelligent signal control, safety and energy applications, and cooperate driving applications. The intelligent roadway infrastructure approach, as opposed to a vehicle-centric approach, is more scalable because it can be deployed to the roughly 300,000 signalized intersections more readily than over 300 million vehicles in the United States, and accrues early-stage benefits equitable to all roadway users addressing safety, equity, fuel efficiency, and greenhouse gas reduction.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2016

Sequential programmable self-assembly: Role of cooperative interactions

Here, we propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenient platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Coarse-grained molecular simulations of allosteric cooperativity

Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

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

Designing for cooperative grain boundary segregation in multicomponent alloys

Tailoring the nanoscale distribution of chemical species at grain boundaries is a powerful method to dramatically influence the properties of polycrystalline materials. However, classical approaches to the problem have tacitly assumed that only competition is possible between solute species. In this paper, we show that solute elements can cooperate in the way they segregate to grain boundaries: In properly targeted alloys, the different chemical species cooperate to each fill complementary grain boundary sites disfavored by the other. By developing a theoretical “spectral” approach to this problem based on quantum-accurate grain boundary site distributions, we show how grain boundaries can be cooperatively alloyed, whether by depletion or enrichment. We provide machine-learned cosegregation information for over 700 ternary aluminum-based alloys and experimentally validate the concept in one ternary alloy where cosegregation is not expected by prior models but is expected based on the cooperative model.

grain boundaries↗
DOE OSTI2019

Cooperative DNA binding by proteins through DNA shape complementarity

Abstract Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein–protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis β-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Vibrational Cooper minima used to verify the dissociation pathway induced by a short intense laser pulse

Vibrational Cooper minima due to weak dipole coupling were previously observed in strong-field dissociation of H 2⁡ + as minima in the kinetic-energy-release (KER) spectrum [McKenna et al., Phys. Rev. Lett. 103, 103006 (2009)]. We demonstrate in two independent experiments that these vibrational Cooper minima occur more generally and can be used as “fingerprints” to identify the final electronic state in the dissociation pathway. In the first experiment, we show the wavelength dependence of the vibrational Cooper minima observed in the KER spectrum of O 2⁢ + dissociation induced by 396- and 264-nm photons. These minima appear at the locations predicted by our first-order perturbation-theory calculations. In the second experiment, a delay-dependent KER spectrum is obtained from O 2 using an ionizing pump and a dissociating probe, then Fourier-transformed to generate a spin-rotation quantum beat spectrum of O 2 ⁢+ . As a result, this spectrum shows vibrational Cooper minima at the expected locations, confirming their presence in another observable. In this case, these minima are used to identify the dissociation pathway.

Molecular dissociation↗
DOE OSTI2025

Solid-state platform for cooperative quantum dynamics driven by correlated emission

While traditionally regarded as an obstacle to quantum coherence, recent breakthroughs in quantum optics have shown that the dissipative interaction of a qubit with its environment can be leveraged to protect quantum states and synthesize many-body entanglement. Inspired by this progress, here we set the stage for the—as yet uncharted—exploration of analogous cooperative phenomena in hybrid solid-state platforms. We develop a comprehensive formalism for the quantum many-body dynamics of an ensemble of solid-state spin defects interacting with the magnetic field fluctuations of a common solid-state reservoir. Our framework applies to any solid-state reservoir whose fluctuating spin, pseudospin, or charge degrees of freedom generate magnetic fields. To understand whether correlations induced by dissipative processes can play a relevant role in a realistic experimental setup, we apply our model to a qubit array interacting via the spin fluctuations of a ferromagnetic bath. Our results show that the low-temperature collective relaxation rates of the qubit ensemble can display clear signatures of super- and subradiance, i.e., forms of cooperative dynamics traditionally achieved in atomic ensembles. We find that the solid-state analog of these cooperative phenomena is robust against spatial disorder in the qubit ensemble and thermal fluctuations of the magnetic reservoir, providing a route for their feasibility in near-term experiments. Finally, our work lays the foundation for a multiqubit approach to quantum sensing of solid-state systems and the direct generation of many-body entanglement in spin-defect ensembles. Furthermore, we discuss how the tunability of solid-state reservoirs opens up novel pathways for exploring cooperative phenomena in regimes beyond the reach of conventional quantum optics setups.

NV centers↗
DOE OSTI2025

Bringing Different Views Together: A Hybrid Cooperative Perception Framework for Connected Autonomous Vehicles

Cooperative perception will be essential for connected autonomous vehicles to enhance object recognition and optimize path planning by sending data information about the surrounding environment. However, an inherent challenge in existing systems is the high bandwidth cost of transmitting information in real-time, which restricts cooperative perception’s practicality. Here, this work presents a hybrid cooperative perception fusion framework aimed at mitigating this issue by optimizing data transmission according to available bandwidth or through data reduction techniques. Our methods ensure that vehicles can rapidly transmit high-confidence data without overwhelming the network. Experimental results indicate that our methodology substantially diminishes data transmission sizes while maintaining object detection accuracy. For cooperative perception in autonomous vehicle systems, our approach provides a scalable and effective way to get past the bandwidth barrier.

Carrillo, Dominic [Univ. of North Texas, Denton, T↗
DOE OSTI2018

Data for Cooperative Asymmetric Reactions Combining Photocatalysis and Enzymatic Catalysis

Living organisms rely on simultaneous reactions catalysed by mutually compatible and selective enzymes to synthesize complex natural products and other metabolites. To combine the advantages of these biological systems with the reactivity of artificial chemical catalysts, chemists have devised sequential, concurrent, and cooperative chemoenzymatic reactions that combine enzymatic and artificial catalysts. Cooperative chemoenzymatic reactions consist of interconnected processes that generate products in yields and selectivities that cannot be obtained when the two reactions are carried out sequentially with their respective substrates. However, such reactions are difficult to develop because chemical and enzymatic catalysts generally operate in different media at different temperatures and can deactivate each other. Owing to these constraints, the vast majority of cooperative chemoenzymatic processes that have been reported over the past 30 years can be divided into just two categories: chemoenzymatic dynamic kinetic resolutions of racemic alcohols and amines, and enzymatic reactions requiring the simultaneous regeneration of a cofactor. New approaches to the development of chemoenzymatic reactions are needed to enable valuable chemical transformations beyond this scope. Here we report a class of cooperative chemoenzymatic reaction that combines photocatalysts that isomerize alkenes with ene-reductases that reduce carbon–carbon double bonds to generate valuable enantioenriched products. This method enables the stereoconvergent reduction of E/Z mixtures of alkenes or reduction of the unreactive stereoisomers of alkenes in yields and enantiomeric excesses that match those obtained from the reduction of the pure, more reactive isomers. The system affords a range of enantioenriched precursors to biologically active compounds. More generally, these results show that the compatibility between photocatalysts and enzymes enables chemoenzymatic processes beyond cofactor regeneration and provides a general strategy for converting stereoselective enzymatic reactions into stereoconvergent ones.

Catalysis↗
DOE OSTI2016

Predicting Human Cooperation

The Prisoner’s Dilemma has been a subject of extensive research due to its importance in understanding the ever-present tension between individual self-interest and social benefit. A strictly dominant strategy in a Prisoner’s Dilemma (defection), when played by both players, is mutually harmful. Repetition of the Prisoner’s Dilemma can give rise to cooperation as an equilibrium, but defection is as well, and this ambiguity is difficult to resolve. The numerous behavioral experiments investigating the Prisoner’s Dilemma highlight that players often cooperate, but the level of cooperation varies significantly with the specifics of the experimental predicament. We present the first computational model of human behavior in repeated Prisoner’s Dilemma games that unifies the diversity of experimental observations in a systematic and quantitatively reliable manner. Our model relies on data we integrated from many experiments, comprising 168,386 individual decisions. The model is composed of two pieces: the first predicts the first-period action using solely the structural game parameters, while the second predicts dynamic actions using both game parameters and history of play. Our model is successful not merely at fitting the data, but in predicting behavior at multiple scales in experimental designs not used for calibration, using only information about the game structure. As a result, we demonstrate the power of our approach through a simulation analysis revealing how to best promote human cooperation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

DOE/UCAR Cooperative Agreement for the Regional and Global Climate Modeling Program

This progress report describes research supported by Cooperative Agreement between the University Corporation for Atmospheric Research (UCAR) and the U.S. Department of Energy (DOE) Biological and Environmental Research (BER). The purpose of the Cooperative Agreement is to provide support for an integrated research program to address key science questions relevant to the DOE Regional and Global Climate Modeling Program as part of the U.S. Global Change Research Program (USGCRP). The Cooperative Agreement funds four tasks that address key aspects of climate science, and this report provides a summary of activities for each task during the past year. As part of the Cooperative Agreement supported science, the Climate Change Prediction (CCP) group at the National Center for Atmospheric Research (NCAR), provides leadership to the Community Earth System Model (CESM) Climate Variability and Change Working Group (CVCWG) through co-chairs Gerald Meehl and Susan Bates (with DOE-funded co-chair Peter Gleckler, along with Clara Deser and Shang-Ping Xie). Over the past year CCP has played a leadership role in performing climate change simulations and analyses with the Community Climate System Model version 4 (CCSM4) and CESM version 1. These simulations and analyses made strong contributions to the federal USGCRP in several high priority areas. We have also been involved in planning for the sixth phase of the Coupled Model Intercomparison Project (CMIP6) which started in 2015. Simulations from CMIP6 will form the basis for ongoing U.S. National Assessment activities, and the IPCC AR6.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1986

The changing face of international space cooperation - One view of NASA

It is pointed out that from its earliest years NASA has incorporated international participation into many of its programs. Guidelines were developed with the objective to maximize the benefits of international cooperation. The cooperative guidelines were accepted because they reflected conditions which applied during much or all of the 1960-1980 period. There existed a clear technology and experience gap between the U.S. and even its largest cooperative partners. Thus, the U.S. enjoyed a virtual Free World monopoly on launching large satellites, especially those destined for geostationary or interplanetary orbits. However, on the basis of new developments, NASA faces now a modified international operating environment, in which the U.S. technological lead has been significantly reduced. The results of this situation are examined, taking into account the equalization of capabilities, the rise of commercial competition, Soviet competition, multinational patterns, and reduced cooperative opportunities.

Pedersen, K. S.↗
NASA NTRS1987

International cooperation in planetary exploration - Past success and future prospects

A review is given of the ways in which the National Aeronautics and Space Administration (NASA) has participated in international efforts to explore the solar system. Past examples of successful international cooperative programs are described. Prospects for future cooperative efforts are discussed with emphasis placed on current events, issues, and trends which are likely to affect possibilities for cooperation over the next 5 to 10 years. Key factors which will play a major role in shaping future prospects for cooperation include the move towards balancing the budget in the United States and the impact of the Challenger accident on the NASA program.

Rosendhal, Jeffrey D.↗