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DOE OSTI2015

DEAD-box helicase DDX27 regulates 3′ end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex

PeBoW, a trimeric complex consisting of pescadillo (Pes1), block of proliferation (Bop1), and the WD repeat protein 12 (WDR12), is essential for processing and maturation of mammalian 5.8S and 28S ribosomal RNAs. Applying a mass spectrometric analysis, we identified the DEAD-box helicase DDX27 as stably associated factor of the PeBoW-complex. DDX27 interacts with the PeBoW-complex via an evolutionary conserved F×F motif in the N-terminal domain and is recruited to the nucleolus via its basic C-terminal domain. This recruitment is RNA-dependent and occurs independently of the PeBoW-complex. Interestingly, knockdown of DDX27, but not of Pes1, induces the accumulation of an extended form of the primary 47S rRNA. We conclude that DDX27 can interact specifically with the Pes1 and Bop1 but fulfils critical function(s) for proper 3′ end formation of 47S rRNA independently of the PeBoW-complex. - Highlights: • DEAD-box helicase DDX27 is a new constituent of the PeBoW-complex. • The N-terminal F×F motif of DDX27 interacts with the PeBoW components Pes1 and Bop1. • Nucleolar anchoring of DDX27 via its basic C-terminal domain is RNA dependent. • Knockdown of DDX27 induces a specific defect in 3′ end formation of 47S rRNA.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation

Highlights: • Radiation increases cellular uptake of exosomes. • Radiation induces colocalization of CD29 and CD81. • Exosomes selectively bind the CD29/CD81 complex. • Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation. - Abstract: Exosomes mediate intercellular communication, and mesenchymal stem cells (MSC) or their secreted exosomes affect a number of pathophysiologic states. Clinical applications of MSC and exosomes are increasingly anticipated. Radiation therapy is the main therapeutic tool for a number of various conditions. The cellular uptake mechanisms of exosomes and the effects of radiation on exosome–cell interactions are crucial, but they are not well understood. Here we examined the basic mechanisms and effects of radiation on exosome uptake processes in MSC. Radiation increased the cellular uptake of exosomes. Radiation markedly enhanced the initial cellular attachment to exosomes and induced the colocalization of integrin CD29 and tetraspanin CD81 on the cell surface without affecting their expression levels. Exosomes dominantly bound to the CD29/CD81 complex. Knockdown of CD29 completely inhibited the radiation-induced uptake, and additional or single knockdown of CD81 inhibited basal uptake as well as the increase in radiation-induced uptake. We also examined possible exosome uptake processes affected by radiation. Radiation-induced changes did not involve dynamin2, reactive oxygen species, or their evoked p38 mitogen-activated protein kinase-dependent endocytic or pinocytic pathways. Radiation increased the cellular uptake of exosomes through CD29/CD81 complex formation. These findings provide essential basic insights for potential therapeutic applications of exosomes or MSC in combination with radiation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Learning from nature’s plant engineers: Hijacking metabolism and development beyond genetics

Plant metabolism underpins the food, fiber, and fuel that support our economy, driving strong interest in new strategies to rewire plant metabolism for emerging applications. While most synthetic biology efforts are reliant on genetic engineering, plants can be manipulated in many other ways that remain comparatively underexplored. Across nature, diverse organisms, including bacteria, fungi, and insects, have evolved sophisticated mechanisms to exploit plant metabolic richness, reshaping it for purposes that span from basic nutrition to the construction of complex, novel structures for shelters. These interspecies interactions and non-model systems represent unique manners in which plants can be reprogrammed or hijacked by other organisms, offering inspiration for novel approaches to engineering plant metabolism. By better understanding the basis of how organisms induce these remarkable transformations in plants, we can expand the conceptual boundaries of synthetic biology and reveal alternative routes to manipulating plants for the production of a diverse array of valuable compounds and materials. Deeper insight into these mechanisms will yield novel blueprints for rethinking the scope and breadth in which we can redesign plant metabolism across many applications.

Sarkiss, Anthony E. [University of California, Ber↗

DOE OSTI2016

Current understanding of interactions between nanoparticles and the immune system

The delivery of drugs, antigens, and imaging agents benefits from using nanotechnology-based carriers. The successful translation of nanoformulations to the clinic involves thorough assessment of their safety profiles, which, among other end-points, includes evaluation of immunotoxicity. The past decade of research focusing on nanoparticle interaction with the immune system has been fruitful in terms of understanding the basics of nanoparticle immunocompatibility, developing a bioanalytical infrastructure to screen for nanoparticle-mediated immune reactions, beginning to uncover the mechanisms of nanoparticle immunotoxicity, and utilizing current knowledge about the structure–activity relationship between nanoparticles' physicochemical properties and their effects on the immune system to guide safe drug delivery. In the present review, we focus on the most prominent pieces of the nanoparticle–immune system puzzle and discuss the achievements, disappointments, and lessons learned over the past 15 years of research on the immunotoxicity of engineered nanomaterials. - Graphical abstract: API — active pharmaceutical ingredient; NP — nanoparticles; PCP — physicochemical properties, CARPA — complement activation-related pseudoallergy, ICH — International Conference on Harmonization. Display Omitted - Highlights: • Achievements, disappointments and lessons learned over past decade are reviewed. • Areas in focus include characterization, immunotoxicity and utility in drug delivery. • Future direction focusing on mechanistic immunotoxicity studies is proposed.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Insights into the Oxidation Mechanism of Vivianite to Metavivianite from First-Principles Calculations

Vivianite, a hydrous ferrous iron-phosphate mineral (Fe 3 (PO 4 ) 2 ·8H 2 O), readily oxidizes in contact with air yielding the less hydrous mixed-valent iron-phosphate mineral metavivianite. This topotactic transformation nominally occurs by oxidative dehydrogenation in which outgoing electrons from the iron sublattice are charge compensated by hydrolysis of structural water. However, the details of this internal charge balancing mechanism that allows the structure to remain electrostatically stable remain unknown. Here, in this study, we use density functional theory (DFT) calculations and ab initio thermodynamics (AIT) to evaluate the energetics of this process in terms of hydrogen release as a function of environmental variables such as partial pressure and temperature. The results show a thermodynamic driving force for vivianite phase transformation as oxidation progresses that is triggered by its rigid structure that has a limited accommodation for hydrogen vacancies. In contrast, metavivianite has a more flexible lattice and hydrogen bond network that stabilizes these hydrogen defects. Metavivianite is shown to be a stable intermediate for 66% residual Fe 2+ down to 33% Fe 2+ , below which other phases/structures such as santabarbarite should be more thermodynamically favorable. Our study provides a basis for experimental tests of our mechanistic findings and helps fill a basic knowledge gap about the solid-state process that defines how vivianite interacts with its surrounding environment.

Sassi, Michel [Pacific Northwest National Laborato↗

DOE OSTI2019

Chiral molecules and the electron spin

The electron’s spin is necessary to the stability of matter, and control over the spin opens up avenues for manipulating the properties of molecules and materials. The Pauli exclusion principle requires that two electrons in a single spatial eigenstate have opposite spins, and this fact dictates basic features of atomic states and chemical bond formation. The energy associated with interacting electron clouds changes with their relative spin orientation, and by manipulating the spin directions, one can guide chemical transformations. However, controlling the relative spin orientation of electrons located on two reactants (atoms, molecules or surfaces) has proved challenging. Recent developments based on the chiral-induced spin selectivity (CISS) effect show that the spin orientation is linked to molecular symmetry and can be controlled in ways not previously imagined. For example, the combination of chiral molecules and electron spin opens up a new approach to (enantio)selective chemistry. Our Review describes the theoretical concepts underlying the CISS effect and illustrates its importance by discussing some of its manifestations in chemistry, biology and physics. Specifically, we discuss how the CISS effect allows for efficient long-range electron transfer in chiral molecules and how it affects biorecognition processes. Several applications of the effect are presented, and the importance of controlling relative spin orientations in multi-electron processes, such as electrochemical water splitting, is emphasized. We describe the enantiospecific interaction between ferromagnetic substrates and chiral molecules and how it enables the separation of enantiomers with ferromagnets. Lastly, we discuss the relevance of CISS effects to biological electron transfer, enantioselectivity and CISS-based spintronics applications.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Evolution of rogue waves in dusty plasmas

The evolution of rogue waves associated with the dynamics of positively charged dust grains that interact with streaming electrons and ions is investigated. Using a perturbation method, the basic set of fluid equations is reduced to a nonlinear Schrödinger equation (NLSE). The rational solution of the NLSE is presented, which proposed as an effective tool for studying the rogue waves in Jupiter. It is found that the existence region of rogue waves depends on the dust-acoustic speed and the streaming densities of the ions and electrons. Furthermore, the supersonic rogue waves are much taller than the subsonic rogue waves by ∼25 times.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Ultrafast dynamics of spin and orbital correlations in quantum materials: an energy- and momentum-resolved perspective

Many remarkable properties of quantum materials emerge from states with intricate coupling between the charge, spin and orbital degrees of freedom. Ultrafast photo-excitations of these materials hold great promise for understanding and controlling the properties of these states. Here we introduce time-resolved resonant inelastic X-ray scattering (tr-RIXS) as a means of measuring the charge, spin and orbital excitations out of equilibrium. These excitations encode the correlations and interactions that determine the detailed properties of the states generated. After outlining the basic principles and instrumentation of tr-RIXS, we review our first observations of transient antiferromagnetic correlations in quasi two dimensions in a photo-excited Mott insulator and present possible future routes of this fast-developing technique. The increasing number of X-ray free electron laser facilities not only enables tackling long-standing fundamental scientific problems, but also promises to unleash novel inelastic X-ray scattering spectroscopies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

An Approach to Realize Generalized Optimal Motion Primitives Using Physics Informed Neural Networks

Autonomous manipulation is a challenging problem in field robotics due to uncertainty in object properties, constraints, and coupling phenomenon with robot control systems. Humans learn motion primitives over time to effectively interact with the environment. We postulate that autonomous manipulation can be enabled by basic sets of motion primitives as well, but do not necessitate mimicking human motion primitives. Here, this work presents an approach to generalized optimal motion primitives using physics-informed neural networks. Our simulated and experimental results demonstrate that optimality is notionally maintained where the mean maximum observed final position percent error was 0.564% and the average mean error for all the trajectories was 1.53%. These results indicate that notional generalization is attained using a physics-informed neural network approach that enables near optimal real-time adaptation of primitive motion profiles.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Precision Measurement of Electroproduction of pi 0 near Threshold

Electromagnetic production of neutral pions near threshold is the most basic, lowest energy reaction in which a new hadron is created. The electromagnetic interaction is well understood so measurements of this reaction can yield direct insight into the hadronic production mechanism. During the past three decades there have been many developments in both the measurement and theory of threshold pion production, starting with measurements of photo-production at Saclay in 1986 and at Mainz in 1990. These measurements indicated a surprising discrepancy with so-called Low Energy Theorems (LETs) which are based on quite fundamental symmetries and considerations. Chiral Perturbation Theory (ChPT) is an effective field theoretic description of the nuclear force which contains the underlying symmetries of the force but deals with nucleons and pions rather than quarks and gluons. It has the advantage of being applicable at low energies but requires tuning some parameters to experimental data. Once these parameters have been determined ChPT predicts how the reaction should behave as a function of the kinematic variable. When applied to the reaction, p(γ,π 0 )p, near threshold it explained the discrepancy with the LETs and made predictions for electroproduction, p(e,e'p)π 0 . Electroproduction measurements at Mainz in the 1990's showed a clear discrepancy with these predictions of ChPT; with parameters determined from one set of kinematics the data for a second set lay far from the predicted value. However, recently completed measurements at Mainz disagreed with their previous measurements. In the experiment presented here, measurements of neutral pion electroproduction,p(e,e'p)π 0 , were made in bins of momentum transfer, Q 2 , between Q 2 = 0.05 [GeV/c] 2 and Q 2 = 0.15 [GeV/c] 0 and of center-of-mass energy, W, between 0 ≤ W ≤ 30 MeV (above threshold). The experiment was performed in Hall A at the Jefferson Laboratory. Scattered electrons were detected in one of the two High Resolution Spectrometers while the recoiling protons were detected in the BigBite spectrometer. The results of the present experiment agree within uncertainties with the recent Mainz measurements and extend in W significantly beyond those measurements. The present data show significant disagreement with some terms in the cross section above Q 2 ~ 0.10 [GeV/c] 2 . For W ≥ 5 MeV the disagreement is very strong and consistent. Whether fitting new ChPT parameters to the recent data or adding more terms to the calculations would improve the agreement remains to be seen.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1972

Computerized optimal control system design for reusable and expendable boost vehicles.

An optimization technique has been developed which combines the practical features of hybrid simulation of the dynamic system under study with the systematic approach of modern control theory where a mathematically formulated design criterion is optimized by functional minimization. Standard hybrid computer optimization methods using high-speed repetitive simulations and gradient minimization schemes have been extended to obtain time-varying optimal gain schedules and reduce the sensitivity of the optimized system to parameter and disturbance uncertainties. In this approach the performance index is expressed in meaningful engineering terms that reflect the interactions among all major disciplines, structures, control/actuation system design, aerodynamics and performance. The basic optimization technique is developed and its application to current aerospace control problems including the space shuttle is presented in detail. In the discussion of the application, the controllers resulting from the technique are compared with controllers developed by conventional methods. The paper concludes with a review of the advantages and disadvantages of the technique and plans for future applications.

Connor, C. L.↗

NASA NTRS1974

Study of ballistic mode comet Encke mission opportunities

An analysis was conducted of the space mission to intercept the comet Encke. The two basic types of flight geometry considered for the mission are described. The primary interactions between time-of-flight and performance characteristics are displayed. The representative spacecraft characteristics for the Titan 3/Centaur launch vehicle are tabulated. The navigation analyses for the two missions are developed to show: (1) assessment of the navigation feasibility of the missions, (2) determination of the total velocity budget for the trim maneuvers, and (3) evaluation of dispersions at comet encounter.

Hollenbeck, G. R.↗

NASA NTRS1979

Modeling and control of a LN2-GN2 operated closed circuit cryogenic wind tunnel

An explicit but simple lumped parameter nonlinear multivariable model of a LN2-GN2-operated closed circuit cryogenic wind tunnel has been developed and its basic features have been experimentally validated. The model describes the mass-energy interaction involved in the cryogenic tunnel process and includes the real gas properties of nitrogen gas.

Balakrishna, S.↗

NASA NTRS1982

Assessment of turbulent models for scramjet flowfields

The behavior of several turbulence models applied to the prediction of scramjet combustor flows is described. These models include the basic two equation model, the multiple dissipation length scale variant of the two equation model, and the algebraic stress model (ASM). Predictions were made of planar backward facing step flows and axisymmetric sudden expansion flows using each of these approaches. The formulation of each of these models are discussed, and the application of the different approaches to supersonic flows is described. A modified version of the ASM is found to provide the best prediction of the planar backward facing step flow in the region near the recirculation zone, while the basic ASM provides the best results downstream of the recirculation. Aspects of the interaction of numerica modeling and turbulences modeling as they affect the assessment of turbulence models are discussed.

Sindir, M. M.↗

NASA NTRS1988

Interactive grid generation for turbomachinery flow field simulations

The control point form of algebraic grid generation presented provides the means that are needed to generate well structured grids for turbomachinery flow simulations. It uses a sparse collection of control points distributed over the flow domain. The shape and position of coordinate curves can be adjusted from these control points while the grid conforms precisely to all boundaries. An interactive program called TURBO, which uses the control point form, is being developed. Basic features of the code are discussed and sample grids are presented. A finite volume LU implicit scheme is used to simulate flow in a turbine cascade on the grid generated by the program.

Choo, Yung K.↗

NASA NTRS1988

Interactive grid generation for turbomachinery flow field simulations

The control point form of algebraic grid generation presented provides the means that are needed to generate well structured grids of turbomachinery flow simulations. It uses a sparse collection of control points distributed over the flow domain. The shape and position of coordinate curves can be adjusted from these control points while the grid conforms precisely to all boundaries. An interactive program called TURBO, which uses the control point form, is being developed. Basic features of the code are discussed and sample grids are presented. A finite volume LU implicit scheme is used to simulate flow in a turbine cascade on the grid generated by the program.

Choo, Yung K.↗

NASA NTRS1990

Direct simulation of turbulent combustion

Understanding and modeling of turbulent combustion are key-problems in the computation of numerous practical systems. Because of the lack of analytical theories in this field and of the difficulty of performing precise experiments, direct simulation appears to be one of the most attractive tools to use in addressing this problem. The present work can be split into two parts: (1) Development and validation of a direct simulation method for turbulent combustion; (2) Applications of the method to premixed turbulent combustion problems. The goal of part 1 is to define and to test a numerical method for direct simulation of reacting flows. A high level of confidence should be attached to direct simulation results, and this can only be achieved through extensive validation tests. In part 2, direct simulation is used to address some of the many critical problems related to turbulent combustion. At the present time, I have limited this work to premixed combustion and considered only four basic issues: (1) The effect of pressure waves on flame propagation; (2) The interaction between flame fronts and vortices; (3) The influence of curvature on premixed flame fronts; and (4) The validation of flamelet models for premixed turbulent combustion.

Poinsot, T. J.↗

NASA NTRS1992

Recent results from studies of electron beam phenomena in space plasmas

The paper examines selected results from experiments, performed in 1980s, involving the ejection of beams of electrons from spacecraft. Special attention is given to the basic processes associated with the spacecraft charging, passive current collection, beam-atmosphere interactions, beam-plasma interactions, and neutral gas emission. Consideration is also given to future experiments on active electron beam ejections in space.

Neubert, Torsten↗