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At least 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Organophilic, Superparamagnetic, and Reversibly Thermoresponsive Silica-Polypeptide Core–Shell Particles

Particles with a superparamagnetic cobalt inner core, silica outer core, and covalently bound homopolypeptide shell were investigated under thermal and magnetic stimuli. The homopolypeptide was poly(ε-carbobenzyloxy- l -lysine), PCBL, which is known to exhibit a thermoreversible coil ⇔ helix transition when dissolved as a pure polymer in m- cresol. Tethering to a core particle did not prevent PCBL from undergoing this conformational transition, as confirmed by dynamic light scattering and optical rotation, but the transition was broadened compared to that of the untethered polymer. The Co@SiO 2 -PCBL hybrid particles retained the superparamagnetic properties of the cobalt inner nougat. Indeed, some response remains even after aging for >5 years. The aged PCBL shell also preserved its responsiveness to temperature, although differences in the shape of the size vs temperature transition curve were determined compared to the freshly made particles. A reversible coil ⇔ helix transition for a particle-bound polypeptide in a pure organic solvent is rare. Further to providing a convenient tool for characterizing coil ⇔ helix transitions for surface-bound polypeptides without interference from pH or the strong ionic forces that dominate behavior in aqueous systems, the Co@SiO 2 -PCBL/ m -cresol system may prove useful in studies of the effect of shell polymer conformation on colloid interactions. The stability of the magnetic core and polypeptide shell suggest a long shelf life for Co@SiO 2 -PCBL, which can, in principle, be deprotected to yield positively charged Co@SiO 2 -poly( l -lysine) particles for possible transfection or antimicrobial applications or chained magnetically to produce responsive poly(colloids).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Time-Evolving Chirality Loss in Molecular Photodissociation Monitored by X-ray Circular Dichroism Spectroscopy

In this work, the ultrafast photoinduced chirality loss of 2-iodobutane is studied theoretically by time- and frequency-resolved X-ray circular dichroism (TRXCD) spectroscopy. Following an optical excitation, the iodine atom dissociates from the chiral center, which we capture by quantum non-adiabatic molecular dynamics simulations. At variable time delays after the pump, the resonant X-ray pulse selectively probes the iodine and carbon atom involved in the chiral dissociation through a selected core-to-valence transition. The TRXCD signal at the iodine L 1 edge accurately captures the timing of C–I photodissociation and thereby chirality loss, c.a 70 fs. The strong electric dipole–electric quadrupole (ED–EQ) response makes this signal particularly sensitive to vibronic coherence at the high X-ray regime. At the carbon K-edges, the signals monitor the molecular chirality of the 2-butyl radical photoproduct and the spin state of the iodine atom. The ED–EQ response is masked under the strong electric dipole-magnetic dipole response, making this signal intuitive for the electronic population. The evolution of the core electronic states and its chiral sensitivity is discussed. Overall, the element-specific TRXCD signal provides a detailed picture of molecular dynamics and offers a unique sensitive window into the time-dependent chirality of molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1988

Numerical simulations of thermal-chemical instabilities at the core-mantle boundary

Numerical simulations of thermal-chemical instabilities in the D-double-prime layer at the core-mantle boundary are presented which show that strong lateral heterogeneities in the composition and density fields can be initiated and maintained dynamically if there is continuous replenishment of material from subduced slabs coming from the upper mantle. These chemical instabilities have a tendency to migrate laterally and may help to support core-mantle boundary topography with short and long wavelengths. The thermal-chemical flows produce a relatively stagnant D-double-prime layer with strong lateral and temporal variations in basal heat flux, which gives rise to thermal core-mantle interactions influencing the geodynamo.

Hansen, Ulrich↗
DOE OSTI2023

Applying the core-satellite species concept: Characteristics of rare and common riverine dissolved organic matter

Introduction: Dissolved organic matter (DOM) composition varies over space and time, with a multitude of factors driving the presence or absence of each compound found in the complex DOM mixture. Compounds ubiquitously present across a wide range of river systems (hereafter termed core compounds) may differ in chemical composition and reactivity from compounds present in only a few settings (hereafter termed satellite compounds). Here, we investigated the spatial patterns in DOM molecular formulae presence (occupancy) in surface water and sediments across 97 river corridors at a continental scale using the “Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems—WHONDRS” research consortium. Methods: We used a novel data-driven approach to identify core and satellite compounds and compared their molecular properties identified with Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Results: In this work, we found that core compounds clustered around intermediate hydrogen/carbon and oxygen/carbon ratios across both sediment and surface water samples, whereas the satellite compounds varied widely in their elemental composition. Within surface water samples, core compounds were dominated by lignin-like formulae, whereas protein-like formulae dominated the core pool in sediment samples. In contrast, satellite molecular formulae were more evenly distributed between compound classes in both sediment and water molecules. Core compounds found in both sediment and water exhibited lower molecular mass, lower oxidation state, and a higher degree of aromaticity, and were inferred to be more persistent than global satellite compounds. Higher putative biochemical transformations were found in core than satellite compounds, suggesting that the core pool was more processed. Discussion: The observed differences in chemical properties of core and satellite compounds point to potential differences in their sources and contribution to DOM processing in river corridors. Overall, our work points to the potential of data-driven approaches separating rare and common compounds to reduce some of the complexity inherent in studying riverine DOM.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

DIFFERENT DYNAMICAL AGES FOR THE TWO YOUNG AND COEVAL LMC STAR CLUSTERS, NGC 1805 AND NGC 1818, IMPRINTED ON THEIR BINARY POPULATIONS

The two Large Magellanic Cloud star clusters, NGC 1805 and NGC 1818, are approximately the same chronological age (∼30 Myr), but show different radial trends in binary frequency. The F-type stars (1.3–2.2 M{sub ⊙}) in NGC 1818 have a binary frequency that decreases toward the core, while the binary frequency for stars of similar mass in NGC 1805 is flat with radius, or perhaps bimodal (with a peak in the core). We show here, through detailed N-body modeling, that both clusters could have formed with the same primordial binary frequency and with binary orbital elements and masses drawn from the same distributions (defined from observations of open clusters and the field of our Galaxy). The observed radial trends in binary frequency for both clusters are best matched with models that have initial substructure. Furthermore, both clusters may be evolving along a very similar dynamical sequence, with the key difference that NGC 1805 is dynamically older than NGC 1818. The F-type binaries in NGC 1818 still show evidence of an initial period of rapid dynamical disruptions (which occur preferentially in the core), while NGC 1805 has already begun to recover a higher core binary frequency, owing to mass segregation (which will eventually produce a distribution in binary frequency that rises only toward the core, as is observed in old Milky Way star clusters). This recovery rate increases for higher-mass binaries, and therefore even at one age in one cluster, we predict a similar dynamical sequence in the radial distribution of the binary frequency as a function of binary primary mass.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1997

Application-Controlled Demand Paging for Out-of-Core Visualization

In the area of scientific visualization, input data sets are often very large. In visualization of Computational Fluid Dynamics (CFD) in particular, input data sets today can surpass 100 Gbytes, and are expected to scale with the ability of supercomputers to generate them. Some visualization tools already partition large data sets into segments, and load appropriate segments as they are needed. However, this does not remove the problem for two reasons: 1) there are data sets for which even the individual segments are too large for the largest graphics workstations, 2) many practitioners do not have access to workstations with the memory capacity required to load even a segment, especially since the state-of-the-art visualization tools tend to be developed by researchers with much more powerful machines. When the size of the data that must be accessed is larger than the size of memory, some form of virtual memory is simply required. This may be by segmentation, paging, or by paged segments. In this paper we demonstrate that complete reliance on operating system virtual memory for out-of-core visualization leads to poor performance. We then describe a paged segment system that we have implemented, and explore the principles of memory management that can be employed by the application for out-of-core visualization. We show that application control over some of these can significantly improve performance. We show that sparse traversal can be exploited by loading only those data actually required. We show also that application control over data loading can be exploited by 1) loading data from alternative storage format (in particular 3-dimensional data stored in sub-cubes), 2) controlling the page size. Both of these techniques effectively reduce the total memory required by visualization at run-time. We also describe experiments we have done on remote out-of-core visualization (when pages are read by demand from remote disk) whose results are promising.

Cox, Michael↗
NASA NTRSDate not supplied

A Temporal Differential Dynamic Logic Formal Embedding

Differential dynamic logic is a formal framework to specify and reason about hybrid programs (HPs). The core of dL is a proof calculus that contains a collection of axioms and rules for the rigorous verification of properties of HPs. Recently, dL has been embedded within the theorem prover Prototype Verification System (PVS) resulting in the tool Plaidypvs2. The integration of dL into PVS expands its expressive power; user defined functions, such as trigonometric and other transcendental functions, can be used inside the dL framework, and meta-reasoning about HPs can be performed, including reasoning about entire classes of HPs, specified using dependent types in PVS. The differential temporal dynamic logic (dTL2) extends dL with temporal logic operators to reason about all the states reachable during the execution of an HP. This paper presents a work in progress focusing on embedding dTL2 in PVS as an extension of Plaidypvs. Plaidypvs is expanded with the formalization of a trace semantics for HPs, the definition of the LTL temporal operators eventually and globally, and the implementation of the proof calculus for dTL2. This new embedding has the same capabilties as Plaidypvs, which allows user defined functions and meta-reasoning of properties of HPs. To the best of the authors’ knowledge this is the first implementation of dTL2.

differential dynamic logic↗
DOE OSTI2014

The structure, dynamics, and star formation rate of the Orion nebula cluster

The spatial morphology and dynamical status of a young, still-forming stellar cluster provide valuable clues to the conditions during the star formation event and the processes that regulated it. We analyze the Orion Nebula Cluster (ONC), utilizing the latest censuses of its stellar content and membership estimates over a large wavelength range. We determine the center of mass of the ONC and study the radial dependence of angular substructure. The core appears rounder and smoother than the outskirts, which is consistent with a higher degree of dynamical processing. At larger distances, the departure from circular symmetry is mostly driven by the elongation of the system, with very little additional substructure, indicating a somewhat evolved spatial morphology or an expanding halo. We determine the mass density profile of the cluster, which is well fitted by a power law that is slightly steeper than a singular isothermal sphere. Together with the interstellar medium density, which is estimated from average stellar extinction, the mass content of the ONC is insufficient by a factor ∼1.8 to reproduce the observed velocity dispersion from virialized motions, in agreement with previous assessments that the ONC is moderately supervirial. This may indicate recent gas dispersal. Based on the latest estimates for the age spread in the system and our density profiles, we find that at the half-mass radius, 90% of the stellar population formed within ∼5-8 free-fall times (t {sub ff}). This implies a star formation efficiency per t {sub ff} of ε{sub ff} ∼ 0.04-0.07 (i.e., relatively slow and inefficient star formation rates during star cluster formation).

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2010

Interactions of Ku70/80 with Double-Strand DNA: Energetic, Dynamics, and Functional Implications

Space radiation is a proficient inducer of DNA damage leading to mutation, aberrant cell signaling, and cancer formation. Ku is among the first responding proteins in nucleus to recognize and bind the DNA double strand breaks (DSBs) whenever they are introduced. Once loaded Ku works as a scaffold to recruit other repair factors of non-homologous end joining and facilitates the following repair processes. The crystallographic study of the Ku70/80 heterodimer indicate the core structure of this protein shows virtually no conformational change after binding with DNA. To investigate the dynamical features as well as the energetic characteristics of Ku-DNA binding, we conduct multi-nanosecond molecular dynamics simulations of a modeled Ku70/80 structure and several complexes with two 24-bp DNA duplexes. Free energy calculations show significant energy differences between the complexes with Ku bound at DSBs and those with Ku associated at an internal site of a chromosome. The results also reveal detailed interactions between different nucleotides and the amino acids along the DNA-binding cradle of Ku, indicating subtle binding preference of Ku at specific DNA sequences. The covariance matrix analyses along the trajectories demonstrate the protein is stimulated to undergo correlated motions of different domains once bound to DNA ends. Additionally, principle component analyses identify these low frequency collective motions suitable for binding with and translocation along duplex DNA. It is proposed that the modification of dynamical properties of Ku upon binding with DSBs may provide a signal for the further recruitment of other repair factors such as DNA-PKcs, XLF, and XRCC4.

Hu, Shaowen↗
DOE OSTI2012

IS ACTIVE REGION CORE VARIABILITY AGE DEPENDENT?

The presence of both steady and transient loops in active region cores has been reported from soft X-ray and extreme-ultraviolet observations of the solar corona. The relationship between the different loop populations, however, remains an open question. We present an investigation of the short-term variability of loops in the core of two active regions in the context of their long-term evolution. We take advantage of the nearly full Sun observations of STEREO and Solar Dynamics Observatory spacecraft to track these active regions as they rotate around the Sun multiple times. We then diagnose the variability of the active region cores at several instances of their lifetime using EIS/Hinode spectral capabilities. We inspect a broad range of temperatures, including for the first time spatially and temporally resolved images of Ca XIV and Ca XV lines. We find that the active region cores become fainter and steadier with time. The significant emission measure at high temperatures that is not correlated with a comparable increase at low temperatures suggests that high-frequency heating is viable. The presence, however, during the early stages, of an enhanced emission measure in the ''hot'' (3.0-4.5 MK) and ''cool'' (0.6-0.9 MK) components suggests that low-frequency heating also plays a significant role. Our results explain why there have been recent studies supporting both heating scenarios.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence–structure–function relations remain poorly characterized. Here, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 20 3 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Solar Models with Dynamic Screening and Early Mass Loss Tested by Helioseismic, Astrophysical, and Planetary Constraints

The faint young Sun paradox remains an open question. Presented here is one possible solution to this apparent inconsistency, a more massive early Sun. Based on the conditions on early Earth and Mars, a luminosity constraint is set as a function of mass. For this, we examine helioseismic constraints of these alternative mass-losing models. Additionally, we explore a dynamic electron screening correction in an effort to improve helioseismic agreement in the core of the early mass-losing model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

A performance study of the time-varying cache behavior: a study on APEX, Mantevo, NAS, and PARSEC

Cache has long been used to minimize the latency of main memory accesses by storing frequently used data near the processor. Processor performance depends on the underlying cache performance. Therefore, significant research has been done to identify the most crucial metrics of cache performance. Although the majority of research focuses on measuring cache hit rates and data movement as the primary cache performance metrics, cache utilization is significantly important. We investigate the application’s locality using cache utilization metrics. In addition, we present cache utilization and traditional cache performance metrics as the program progresses providing detailed insights into the dynamic application behavior on parallel applications from four benchmark suites running on multiple cores. We explore cache utilization for APEX, Mantevo, NAS, and PARSEC, mostly scientific benchmark suites. Our results indicate that 40% of the data bytes in a cache line are accessed at least once before line eviction. Also, on average a byte is accessed two times before the cache line is evicted for these applications. Moreover, we present runtime cache utilization, as well as, conventional performance metrics that illustrate a holistic understanding of cache behavior. To facilitate this research, we build a memory simulator incorporated into the Structural Simulation Toolkit (Rodrigues et al. in SIGMETRICS Perform Eval Rev 38(4):37–42, 2011). Finally, our results suggest that variable cache line size can result in better performance and can also conserve power.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Enriched Molecular-Level View of Saline Wetland Soil Carbon by Sensitivity-Enhanced Solid-State NMR

Soil organic matter (SOM) plays a major role in mitigating greenhouse gas emission and regulating earth’s climate, carbon cycle, and biodiversity. Wetland soils account for one-third of all SOM; however, globally, coastal wetland soils are eroding faster due to increasing sea-level rise. Our understanding of carbon sequestration dynamics in wetlands lags behind that of upland soils. Here, we employ solid-state nuclear magnetic resonance (ssNMR) to investigate the molecular-level structure of biopolymers in wetland soils spanning 11 centuries. High-resolution multidimensional spectra, enabled by dynamic nuclear polarization (DNP), demonstrate enduring preservation of molecular structures within herbaceous plant cores, notably condensing aromatic motifs and carbohydrates, even over a millennium, with the preserved cores constituting a decreasing minority among molecules from decomposition and repolymerization with depth and age. Such preserved cores occur alongside molecules from the decomposition of loosely packed parent biopolymers. These findings emphasize the relative vulnerability of coastal wetland SOM when exposed to oxygenated water due to geological and anthropogenic changes.

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

The field of human building interaction for convergent research and innovation for intelligent built environments

Human-Building Interaction (HBI) is a convergent field that represents the growing complexities of the dynamic interplay between human experience and intelligence within built environments. This paper provides core definitions, research dimensions, and an overall vision for the future of HBI as developed through consensus among 25 interdisciplinary experts in a series of facilitated workshops. Three primary areas contribute to and require attention in HBI research: humans (human experiences, performance, and well-being), buildings (building design and operations), and technologies (sensing, inference, and awareness). Three critical interdisciplinary research domains intersect these areas: control systems and decision making, trust and collaboration, and modeling and simulation. Finally, at the core, it is vital for HBI research to center on and support equity, privacy, and sustainability. Compelling research questions are posed for each primary area, research domain, and core principle. State-of-the-art methods used in HBI studies are discussed, and examples of original research are offered to illustrate opportunities for the advancement of HBI research.

42 ENGINEERING↗
DOE OSTI2014

Development and evaluation of a device for simultaneous uniaxial compression and optical imaging of cartilage samples in vitro

In this paper, we present a system that allows imaging of cartilage tissue via optical coherence tomography (OCT) during controlled uniaxial unconfined compression of cylindrical osteochondral cores in vitro. We describe the system design and conduct a static and dynamic performance analysis. While reference measurements yield a full scale maximum deviation of 0.14% in displacement, force can be measured with a full scale standard deviation of 1.4%. The dynamic performance evaluation indicates a high accuracy in force controlled mode up to 25 Hz, but it also reveals a strong effect of variance of sample mechanical properties on the tracking performance under displacement control. In order to counterbalance these disturbances, an adaptive feed forward approach was applied which finally resulted in an improved displacement tracking accuracy up to 3 Hz. A built-in imaging probe allows on-line monitoring of the sample via OCT while being loaded in the cultivation chamber. We show that cartilage topology and defects in the tissue can be observed and demonstrate the visualization of the compression process during static mechanical loading.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

The electronic structure of vanadium monochloride cation (VCl{sup +}): Tackling the complexities of transition metal species

Six electronic states (X {sup 4}Σ{sup −}, A {sup 4}Π, B {sup 4}Δ, {sup 2}Φ, {sup 2}Δ, {sup 2}Σ{sup +}) of the vanadium monochloride cation (VCl{sup +}) are described using large basis set coupled cluster theory. For the two lowest quartet states (X {sup 4}Σ{sup −} and A {sup 4}Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T{sub 0}) and spectroscopic constants (r{sub e}, r{sub 0}, B{sub e}, B{sub 0}, D{sup ¯}{sub e}, H{sub e}, ω{sub e}, v{sub 0}, α{sub e}, ω{sub e}x{sub e}) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X {sup 4}Σ{sup −}), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state ({sup 2}Γ) has a T{sub e} of ∼11 200 cm{sup −1}. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗