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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Information Length Concept Applied to Plasma Turbulence

A methodology to study statistical properties of anomalous transport in fusion plasma is investigated. Three time traces generated by the full-f gyrokinetic code GKNET are analyzed for this purpose. The time traces consist of heat flux as a function of the radial position, which is studied in a novel manner using statistical methods. The simulation data exhibit transport processes with both medium and long correlation length along the radius. A typical example of a phenomenon with long correlation length is avalanches. In order to investigate the evolution of the turbulent state, two basic configurations are studied, one flux-driven and one gradient-driven with decaying turbulence. The information length concept in tandem with Boltzmann–Gibbs and Tsallis entropy is used in the investigation. It is found that the dynamical states in both flux-driven and gradient-driven cases are surprisingly similar, but the Tsallis entropy reveals differences between them. This indicates that the types of probability distribution function are nevertheless quite different since the higher moments are significantly different.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2015

Effects of Unpredictable Variable Prenatal Stress (UVPS) on Bdnf DNA Methylation and Telomere Length in the Adult Rat Brain

In utero exposure to stress can shape neurobiological and behavioral outcomes in offspring, producing vulnerability to psychopathology later in life. Animal models of prenatal stress likewise have demonstrated long-­‐term alterations in brain function and behavioral deficits in offspring. For example, using a rodent model of unpredictable variable prenatal stress (UVPS), in which dams are exposed to unpredictable, variable stress across pregnancy, we have found increased body weight and anxiety-­‐like behavior in adult male, but not female, offspring. DNA methylation (addition of methyl groups to cytosines which normally represses gene transcription) and changes in telomere length (TTAGGG repeats on the ends of chromosomes) are two molecular modifications that result from stress and could be responsible for the long-­‐term effects of UVPS. Here, we measured methylation of brain-­‐derived neurotrophic factor (bdnf), a gene important in development and plasticity, and telomere length in the brains of adult offspring from the UVPS model. Results indicate that prenatally stressed adult males have greater methylation in the medial prefrontal cortex (mPFC) compared to non-­‐stressed controls, while females have greater methylation in the ventral hippocampus compared to controls. Further, prenatally stressed males had shorter telomeres than controls in the mPFC. These findings demonstrate the ability of UVPS to produce epigenetic alterations and changes in telomere length across behaviorally-­‐relevant brain regions, which may have linkages to the phenotypic outcomes.

epigenetic developmental programming↗
DOE OSTI2014

Expansion Behavior and Temperature Mapping of Thermites in Burn Tubes as a Function of Fill Length [Thermal Imaging of Thermite Flame Propagation]

The reaction of loosely-packed aluminum/copper oxide (Al/CuO) thermites in a 12 cm long acrylic burn tube was investigated as a function of the fill length from 2 to 10 cm. The velocity of the luminous front was measured both in the filled and unfilled region, and approached 1000 m s-1 in the unfilled region, independent of the fill length. This value is approximately a factor of two higher than the fastest velocity measured in the filled region, 606 m s-1, for the 10 cm filled tube. The velocity increase in the unfilled region ist likely due to the increased open porosity, which can support faster flow velocities for a given pressure gradient relative to that in the porous material. A high-speed color imaging pyrometer was used to thermally map the evolution of the flame in both regions. Near the luminous front in the filled section, the temperature was observed to rapidly increase in a 1–2 cm zone to a maximum value near 3200 K, and an average value near 3000 K was sustained in the wake well after the front passes and exits the tube. In partially-filled tubes, even for the lowest fill length of 2 cm, the intermediate and/or product species could be seen to expand forward and completely fill the tube with a sustained temperature of ca. 3000 K. This temperature did not decay during the expansion, suggesting that the material continues to react as it expands. The results raise several questions about what a burn tube experiment is really measuring; such as what fraction of the material has burned when the luminous front passes and what role open cracks or microstructures play in promoting transport. Lastly, these questions are critically important towards developing a predictive capability for confined, loosely packed deflagrations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Energy levels of one-dimensional systems satisfying the minimal length uncertainty relation

The standard approach to calculating the energy levels for quantum systems satisfying the minimal length uncertainty relation is to solve an eigenvalue problem involving a fourth- or higher-order differential equation in quasiposition space. It is shown that the problem can be reformulated so that the energy levels of these systems can be obtained by solving only a second-order quasiposition eigenvalue equation. Through this formulation the energy levels are calculated for the following potentials: particle in a box, harmonic oscillator, Pöschl–Teller well, Gaussian well, and double-Gaussian well. For the particle in a box, the second-order quasiposition eigenvalue equation is a second-order differential equation with constant coefficients. For the harmonic oscillator, Pöschl–Teller well, Gaussian well, and double-Gaussian well, a method that involves using Wronskians has been used to solve the second-order quasiposition eigenvalue equation. It is observed for all of these quantum systems that the introduction of a nonzero minimal length uncertainty induces a positive shift in the energy levels. It is shown that the calculation of energy levels in systems satisfying the minimal length uncertainty relation is not limited to a small number of problems like particle in a box and the harmonic oscillator but can be extended to a wider class of problems involving potentials such as the Pöschl–Teller and Gaussian wells.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Collective motion in prolate γ-rigid nuclei within minimal length concept via a quantum perturbation method

Based on the minimal length concept, inspired by Heisenberg algebra, a closed analytical formula is derived for the energy spectrum of the prolate γ-rigid Bohr–Mottelson Hamiltonian of nuclei, within a quantum perturbation method (QPM), by considering a scaled Davidson potential in β shape variable. In the resulting solution, called X(3)-D-ML, the ground state and the first β-band are all studied as a function of the free parameters. The fact of introducing the minimal length concept with a QPM makes the model very flexible and a powerful approach to describe nuclear collective excitations of a variety of vibrational-like nuclei. The introduction of scaling parameters in the Davidson potential enables us to get a physical minimum of this latter in comparison with previous works. The analysis of the corrected wave function, as well as the probability density distribution, shows that the minimal length parameter has a physical upper bound limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

A novel heme oxygenase-1 splice variant, 14kDa HO-1, promotes cell proliferation and increases relative telomere length

Alternative splicing is a routine phenomenon which greatly increases the diversity of proteins in eukaryotic cells. In humans, most multi-exonic genes are alternatively spliced and their splice variants confer distinct functions. Heme oxygenase-1 (HO-1, 32 kDa) is an inducible stress responsive protein, which possesses multiple functions in many cellular processes. In the current study, we identified a novel alternative splice isoform of 14 kDa HO-1 generated through exclusion of exon 3, and it is highly expressed in immortalized cells. In contrast to nuclear accumulation of the full-length 32 kDa HO-1, the novel 14 kDa HO-1 isoform is retained in the cytoplasm under ultraviolet (UV) irradiation. Interestingly, the 14 kDa HO-1 is shown to promote cell proliferation and an increase in relative telomere lengths in vivo and in vitro. Thus, we are pioneer to report and confirm the presence of a novel splice form of HO-1 and its distinct role in modulating telomere length and tumor growth.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Readthrough of ACTN3 577X nonsense mutation produces full-length α-actinin-3 protein

Highlights: • ACTN3 577X gene expression is suppressed in mammalian cells. • Inhibition of nonsense-mediated mRNA decay (NMD) enhances 577X gene expression. • Aminoglycosides induce readthrough of the 577X codon. • NMD inhibition potentiates aminoglycoside-induced readthrough of the 577X gene. The ACTN3 gene encodes α-actinin-3 protein, which stabilizes the contractile apparatus at the Z-line in skeletal muscle cell fast fibers. A nonsense mutation of the arginine (R) at the codon for amino acid 577 of the ACTN3 gene generates a premature termination codon (PTC) and produces the R577X polymorphism in humans (X specifies translational termination). The ACTN3 577X genotype abolishes α-actinin-3 protein production due to targeted degradation of the mutant transcript by the cellular nonsense-mediated mRNA decay (NMD) system, which requires mRNA splicing. In humans, α-actinin-3 deficiency can decrease sprinting and power performance as well as skeletal muscle mass and strength. Here we investigated whether suppression of the in-frame PTC induced by treatment with the aminoglycosides gentamicin and G418 that promote termination codon readthrough could allow production of full-length α-actinin-3 protein from ACTN3 577X. We constructed expression plasmids encoding mature mRNA that lacks introns or pre-mRNA, which carries introns for the ACTN3 577X gene (X and X{sub pre}, respectively) and transfected the constructs into HEK293 cells. Similar constructs for the ACTN3 577R gene were used as controls. HEK293 cells carrying the X gene, but not the X{sub pre} gene, expressed exogenous truncated α-actinin-3 protein, indicating NMD-mediated suppression of exogenous X{sub pre} expression. Cells treated with aminoglycosides produced exogenous full-length α-actinin-3 protein in X-transfected cells, but not in X{sub pre}-transfected cells. The NMD inhibitor caffeine prevented suppression of X{sub pre} expression and thereby induced production of full-length α-actinin-3 protein in the presence of aminoglycoside. Together these results indicate that the ACTN3 R577X polymorphism could be a novel target for readthrough therapy, which may affect athletic and muscle performance in humans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms

Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from artificial intelligence/machine learning algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Our model is validated by comparing simulated structures with the latest cryo-EM structure detailing close contacts among three key domains and regions of the CRaf. Our simulations identify potentially new epitopes of intramolecule interactions within the CRaf and reveal a dynamical nature of CRaf kinases, in which the three domains can move back and forth relative to each other for regulatory dynamics. The dynamic conformations are then used in a docking algorithm to shed insight into the paradoxical effect caused by vemurafenib in comparison with a paradox breaker PLX7904. In this study, we propose a model of Raf-heterodimer/KRas-dimer as a signalosome based on the dynamics of the full-length CRaf.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Attaining regularization length insensitivity in phase-field models of ductile failure

In this work, a cohesive phase-field model of ductile fracture in a finite-deformation setting is presented. The model is based on a free-energy function in which both elastic and plastic work contributions are coupled to damage. Using a strictly variational framework, the field evolution equations, damage kinetics, and flow rule are jointly derived from a scalar least-action principle. Particular emphasis is placed on the use of a rational function for the stress degradation that maintains a fixed effective strength with decreasing regularization length. The model is employed to examine crack growth in pure mode-I problems through the generation of crack growth resistance (J-R) curves. In contrast to alternative models, the current formulation gives rise to J-R curves that are insensitive to the regularization length. Numerical evidence suggests convergence of local fields with respect to diminishing regularization length as well.

42 ENGINEERING↗
DOE OSTI2021

Supermolecular structures of recrystallized starches with amylopectin side chains modified by amylosucrase to different chain lengths

Understanding the supermolecular structures of recrystallized starches is imperative to manufacture novel starches with controllable physicochemical properties enabling novel applications. In this study, native amylopectin (AP) from maize was modified to different chain lengths using amylosucrase from Neisseria polysaccharea. Native AP granules showed well-organized lamellar structures with a periodicity of ca. 9.0 nm whereas modified starches formed heterogeneous structures with the average crystallite size ranging from 19.77 to 29.88 nm. Acidic treatments eroded amorphous domains in both native AP granules and modified starch particles, producing nanocrystals composed of double helices. A-type nanocrystals (~40 nm) from native AP granules showed quadrangular shape with an acute angle of ca. 60°, while irregular B-type nanocrystals were observed for the modified starches. Molecular characterizations suggested that the nanocrystals had relatively uniform chain lengths (DP 16.5–25.2), and the helix length (the thickness of nanocrystals) was positively correlated to the thermal stability of starches.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Influence of chain length in protic ionic liquids on physicochemical and structural features of lignins from sugarcane bagasse

We report the mechanisms behind lignin dissolution with protic ionic liquids (PILs) and their influence over lignin properties remain not fully explored. In this work, physicochemical and structural features of lignins extracted from sugarcane bagasse after pretreatment with a series of PILs (length of the cation chain combined with different anions) were assessed using analytical techniques. It was found that the lignin extracted with shorter chain length cations PILs showed the highest β-O-4 content. Opposite, the increase of the PILs cation chain length resulted in enhanced depolymerization. All lignins presented high polydispersity (>3.7), while the weight average molecular ranged from 1921 to 13,539 g/mol. The recovered [Eti][Mal] lignin presented the higher β-O-4 content and was possibly the most preserved lignin obtained. Opposite, lignin isolated from [Hex][Ac] and [Hex][For] treatments had less β-O-4 linkages attributed to the depolymerization of lignin via rupture of ether linkages generating intermediates that further repolymerized and/or depolymerized. These results suggest that the ionicity of the PIL is a crucial factor for lignin dissolution. Furthermore, these results illustrate that the proposed pretreatment using different PILs is useful to obtain high-quality lignins with distinct features and opens a new perspective for materials to match various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A predictive strain-gradient model with no undetermined constants or length scales

A general meso–scale (GM) crystal plasticity (CP) model was developed that accounts for lower-order (strain hardening) and higher-order (internal stress) effects of geometrically necessary dislocations (GNDs). It is predictive: no arbitrary parameters or length scales were invoked and no ad hoc numerical techniques were employed. It uses general stress field equations for GND content and a novel harmonization technique to enforce consistency of elastic long-range singular defect fields with applied elastic-plastic fields. The model facilitates implementation in commercial finite element programs without requiring special elements, special boundary conditions, or access to element shape functions. GM simulations confirmed, with improved accuracy, previously published predictions of the Hall-Petch effect, Bauschinger effect, and anelasticity. Previously unpredicted phenomena were also predicted: anelasticity and hysteresis for single Ta crystals and strain-hardening stagnation. The internal stresses (higher-order effect) dominate at large length scales, while at small length scales, the GND density hardening (lower-order effect) dominates. As a result, GM predicts that strain heterogeneity and consequent GND internal stresses are important factors in anelasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Glass length: Workability and meltability of glass as a function of glass melt fragility

Workability and meltability of molten glass are properties important for balancing glass formulation with the design and operations of glass melting and forming facilities. The working and melting “lengths” are the temperature intervals within which glass viscosity allows the melting and forming glass to be performed. They are related to glass melt structure through the glass melt fragility, which, by the augmented Adam-Gibbs equation, is a function of configuration entropy. Both working length and melting length are high for strong glasses and decrease as the melt fragility increases. In this work, analytical formulas are obtained for three-parameter viscosity models VFT, AM, and MYEGA. These models agree with each other and with the Adam-Gibbs equation on the relationship between workability and fragility of glasses but diverge at high-temperatures. The compositional effects on workability and meltability are mediated via the fragility as a function of glass composition expressed in terms of mass and mole component coefficients.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A multi-length-scale investigation of the applicability of ductility laws for annealed and work-hardened copper

Small-scale mechanical testing provides unique advantages over conventional testing in investigating the mechanical response of nuclear materials. While small-scale testing enables accelerated materials research, it raises the question of comparability to large-scale properties for engineering design considerations. Among different mechanical properties for structural design considerations such as yield and ultimate tensile stress, ductility is of critical importance with respect to structural component health. The effectiveness of using small-scale mechanical testing for probing these mechanical properties is dictated by understanding how the mechanical responses translate from the microscale to the engineering scale. Therefore, a better understanding of size scaling effects via gathering and analysis of experimental data is required to bridge length-scales. Further, this work builds upon previous reports to provide statistical data on how mechanical response changes as the size of the specimens are reduced from conventional sizes. One hundred twenty mesoscale tensile coupons of oxygen-free high thermal conductivity (OFHC) copper in work-hardened and annealed state have been manufactured using micro-wire electrical discharge machining (EDM) and tested under uniaxial tension. The mesoscale specimens have dimensions dictated by pre-selected geometric ratios (i.e., gauge section length over the square root of the cross-section area) with gauge length dimensions of 3 mm (or less) and sub-millimeter gauge widths and thicknesses. The mesoscale responses were compared to bulkscale properties to reveal the effect of specimen size on the mechanical response as a function of grain size and material state for a single phase face-centered cubic metal.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Impact of ferromagnetic electrode length and thickness on Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSD)

A knowledge gap exists about the impact of variation in length and thickness of ferromagnetic(FM) electrodes on molecular spintronics devices’ ability to manifest molecular coupling impact. Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSDs) are potential candidates for inventing highly correlated materials and devices and investigating the fundamental science of organic spintronics. This paper reports our experi- mental observations providing the dramatic impact of variation in ferromagnetic electrode length and thickness on paramagnetic molecule-based MTJMSD. Room temperature transport studies were performed to investigate the effect of FM electrode thickness. On the other hand, magnetic force microscopy measurements were con- ducted to understand the effect of FM electrode length extending beyond the molecular junction area, i.e., the site where paramagnetic molecules bridged between two FM. In the strong molecular coupling regime, transport study suggested thickness variation caused ~1000 to million-fold differences in junction conductivity. MFM study revealed near-zero magnetic contrast for pillar-shaped MTJMSD without any extended FM electrode. However, MFM images showed a multitude of microscopic magnetic phases on cross junction shaped MTJMSD where FM electrodes extended beyond the junction area. To understand the intriguing experimental results, we conducted an in-depth theoretical study using Monte Carlo Simulation (MCS) approach. MCS study utilized a Heisenberg atomic model of cross junction shaped MTJMSD to gain insights about room temperature transport and MFM experimental observations of microscopic MTJMSD. To make this study applicable for a wide variety of MTJMSDs, we systematically studied the effect of variation in molecular coupling strength between magnetic molecules and ferromagnetic (FM) electrodes of various dimensions. Here, our theoretical results suggest 25 atoms thick FM electrode show very weak molecular coupling impact and of the same order of experimentally studied FM electrode dimensions showing weak effect. Also, MCS results agree with experimentally observed multiple magnetic phases on lengthy FM electrodes of an MTJMSD.

42 ENGINEERING↗
DOE OSTI2021

Chronic arsenic increases cell migration in BEAS-2B cells by increasing cell speed, cell persistence, and cell protrusion length

Highlights: • Chronic arsenic exposure primes lung epithelial cells for enhanced cell migration. • Chronic arsenic increases cell motility in an EGFR-dependent manner. • Chronic arsenic increases cell persistence in an EGFR-independent manner. • EGFR is sufficient, but not necessary for increasing cell protrusion length in chronic arsenic treated cells. There is a strong association between arsenic exposure and lung cancer development, however, the mechanism by which arsenic exposure leads to carcinogenesis is not clear. In our previous study, we observed that when BEAS-2B cells are chronically exposed to arsenic, there is an increase in secreted TGFα, as well as an increase in EGFR expression and activity. Further, these changes were broadly accompanied with an increase in cell migration. The overarching goal of this study was to acquire finer resolution of the arsenic-dependent changes in cell migration, as well as to understand the role of increased EGFR expression and activity levels in the underlying mechanisms of cell migration. To do this, we used a combination of biochemical and single cell assays, and observed chronic arsenic treatment enhancing cell migration by increasing cell speed, cell persistence and cell protrusion length. All three parameters were further increased by the addition of TGFα, indicating EGFR activity is sufficient to enhance those aspects of cell migration. In contrast, EGFR activity was necessary for the increase in cell speed, as it was reversed with an EGFR inhibitor, AG1478, but was not necessary to enhance persistence and protrusion length. From these data, we were able to isolate both EGFR-dependent and –independent features of cell migration that were enhanced by chronic arsenic exposure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Turbulent entrainment in finite-length wind farms

In this article, we present an entrainment-based model for predicting the flow and power output of finite-length wind farms. The model is an extension of the three-layer approach of Luzzatto-Fegiz & Caulfield ( Phys. Rev. Fluids , vol. 3, 2018, 093802) for wind farms of infinite length, and assumes dependence of key flow quantities, such as the wind farm bulk velocity, on the streamwise distance from the farm entrance. To assist our analysis and validate the proposed model, we undertake a series of large-eddy simulations with different turbine spacing arrangements and layouts. Comparisons are also made with the top-down model with entrance effects of Meneveau ( J. Turbul. , vol. 13, 2012, N7) and data from the literature. The finite-length entrainment model is shown to be capable of capturing the power drop between contiguous rows of turbines as well as describing the advection and turbulent transport of kinetic energy in both the entrance and fully developed regions. The fully developed regime is approximated only deep in the wind farm, after approximately 15 rows of turbines. Our data suggest that for the cases considered in this study, the empirical coefficients that can be used to describe turbulent entrainment and transfers above the wind farm exhibit little dependence on the farm layout and may be considered constant for modelling purposes. However, the flow field within the wind farm layer can be strongly modulated by the turbine density (spacing) as well as the array layout, and to that extent it can be argued that they are both primary factors determining the wind farm power output.

17 WIND ENERGY↗