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At least 343 records · Page 19

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DOE OSTI2015

Dynamics of protein aggregation and oligomer formation governed by secondary nucleation

The formation of aggregates in many protein systems can be significantly accelerated by secondary nucleation, a process where existing assemblies catalyse the nucleation of new species. In particular, secondary nucleation has emerged as a central process controlling the proliferation of many filamentous protein structures, including molecular species related to diseases such as sickle cell anemia and a range of neurodegenerative conditions. Increasing evidence suggests that the physical size of protein filaments plays a key role in determining their potential for deleterious interactions with living cells, with smaller aggregates of misfolded proteins, oligomers, being particularly toxic. It is thus crucial to progress towards an understanding of the factors that control the sizes of protein aggregates. However, the influence of secondary nucleation on the time evolution of aggregate size distributions has been challenging to quantify. This difficulty originates in large part from the fact that secondary nucleation couples the dynamics of species distant in size space. Here, we approach this problem by presenting an analytical treatment of the master equation describing the growth kinetics of linear protein structures proliferating through secondary nucleation and provide closed-form expressions for the temporal evolution of the resulting aggregate size distribution. We show how the availability of analytical solutions for the full filament distribution allows us to identify the key physical parameters that control the sizes of growing protein filaments. Furthermore, we use these results to probe the dynamics of the populations of small oligomeric species as they are formed through secondary nucleation and discuss the implications of our work for understanding the factors that promote or curtail the production of these species with a potentially high deleterious biological activity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction

Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature 1 H– 13 C Heteronuclear Single-Quantum Coherence Zero (HSQC 0 ) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC 0 measurements with yield measurements following depolymerisation, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde-assisted fractionation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction

09 BIOMASS FUELS↗

DOE OSTI2023

Meta-analysis of biogas upgrading to renewable natural gas through biological CO 2 conversion

Biogas upgrading through CO 2 conversion by hydrogenotrophic methanogenesis is receiving an increasing attention worldwide because of the demand for renewable natural gas. Herein, a holistic and statistical study of the operation conditions, driving forces, performances, and potential implementation of biogas upgrading via biological CO 2 conversion was conducted. Based on a systematic review and meta-analysis of 46 existing publications that were selected from 1475 papers, we have compiled a global dataset of CO 2 bioconversion biogas upgrading, encompassing 308 study cases. Subsequently, we employed a rigorous analytical framework incorporating data processing and mixed effects linear regression analysis to examine the dataset. This analysis revealed a significant positive relationship between the H 2 :CO 2 ratio and the methane percentage in the upgraded biogas when using the study as a random effect. Furthermore, we performed meta-analysis on observations taken when the ratio was close to 4:1 and found that ex situ reactors (91.93% [88.11%, 95.75%]) can perform better than in situ reactors (84.74% [80.69%, 88.80%]). No evidence of differential performance was found based on the present dataset between different temperature regimes or operation modes. Furthermore, those findings establish a database that will contribute to a deeper understanding of the biogas upgrading via biological CO 2 conversion.

Biogas upgrading↗

DOE OSTI2025

High-order limiting methods using maximum principle bounds derived from the Boltzmann equation I: Euler equations

The use of limiting methods for high-order numerical approximations of hyperbolic conservation laws generally requires defining an admissible region/bounds for the solution. In this work, we present a novel approach for computing solution bounds and limiting for the Euler equations through the kinetic representation provided by the Boltzmann equation, which allows for extending limiters designed for linear advection directly to the Euler equations. Given an arbitrary set of solution values to compute bounds over (e.g., numerical stencil) and a desired linear advection limiter, the proposed approach yields an analytic expression for the admissible region of particle distribution function values, which may be numerically integrated to yield a set of bounds for the density, momentum, and total energy. Further, these solution bounds are shown to preserve positivity of density/pressure/internal energy and, when paired with a limiting technique, can robustly resolve strong discontinuities while recovering high-order accuracy in smooth regions without any ad hoc corrections (e.g., relaxing the bounds). This approach is demonstrated in the context of an explicit unstructured high-order discontinuous Galerkin/flux reconstruction scheme for a variety of difficult problems in gas dynamics, including cases with extreme shocks and shock-vortex interactions. Furthermore, this work presents a foundation for limiting techniques for more complex macroscopic governing equations that can be derived from an underlying kinetic representation for which admissible solution bounds are not well-understood.

42 ENGINEERING↗

DOE OSTI2021

A process to verify numerical models for seismic fluid-structure interaction in advanced reactor vessels

Seismic design and qualification of a liquid-filled advanced nuclear reactor will have to account for fluid-structure interaction (FSI). Interaction between the tank, internal components, and contained liquid will rely on analysis of numerical models that must be verified and validated. Here this study demonstrates a verification process for models of a base-supported cylindrical tank by comparing numerical predictions and analytical solutions. The numerical models are consistent with the assumptions made to derive analytical solutions, namely, either a rigid or a linear elastic tank, ideal fluid, and small-amplitude, unidirectional, horizontal inputs. One software platform is used to illustrate the process. Seismic FSI analysis is performed using the Arbitrary Lagrangian-Eulerian (ALE) and Incompressible Computational Fluid Dynamics (ICFD) solvers in LS-DYNA. Reported responses are those used for design, including hydrodynamic pressures on the tank wall, shear forces and moments at the tank base, and wave heights of the contained liquid. The accuracy of the numerical results is discussed. The numerical models are verified for calculating the pressures on the tank wall and reactions at its base. Accurate simulation of wave action is challenging for both solvers. Recommendations for modeling, code development, and steps for verification are provided. Although focused on reactor vessels and one software platform, the verification process described herein is broadly applicable to liquid-filled vessels and other finite element codes.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2010

Plasma response to nonlinear time-periodic electric fields in one dimension

Plasma response to spatially nonuniform time-periodic electric fields is of importance in many applications. For the case of a spatially linear monochromatic electric field in Paul traps, exact analytic expressions for the time-dependent plasma distribution function have been recently obtained [K. Shah and H. S. Ramachandran, Phys. Plasmas 15, 062303 (2008)]. In this paper, the problem of plasma response to a one-dimensional time-periodic electric field with a general spatial dependence is considered and analytic expressions for the time-averaged plasma distribution function and density are derived by solving the Vlasov equation under two limiting cases of high and low frequencies. Under this approximation, it is shown that the time-averaged plasma density is a function of the square of the oscillatory electric potential.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2011

A resistive instability of lower hybrid-like waves in regions with parallel currents

The resistive instabilities and dispersion of obliquely propagating waves near the lower hybrid (LH) frequency are studied in plasma carrying a current parallel to the magnetic field. Possible applications of these instabilities include magnetic reconnection regions where LH-like waves may accelerate and heat both ions and electrons. A resistive instability is found in one of the four LH-like wave modes for electron drift speeds several times greater than the electron thermal speed for representative parameters. Numerical fully electromagnetic kinetic calculations of the solutions to the linear dispersion equation are compared with more approximate analytic calculations and show good agreement. The analytic results indicate that ion magnetization effects play a critical role in the resistive instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2012

Quantum ring solitons and nonlocal effects in plasma wake field excitations

A theoretical investigation of the quantum transverse beam motion for a cold relativistic charged particle beam travelling in a cold, collisionless, strongly magnetized plasma is carried out. This is done by taking into account both the individual quantum nature of the beam particles (single-particle uncertainty relations and spin) and the self consistent interaction generated by the plasma wake field excitation. By adopting a fluid model of a strongly magnetized plasma, the analysis is carried out in the overdense regime (dilute beams) and in the long beam limit. It is shown that the quantum description of the collective transverse beam dynamics is provided by a pair of coupled nonlinear governing equations. It comprises a Poisson-like equation for the plasma wake potential (driven by the beam density) and a 2D spinorial Schroedinger equation for the wave function, whose squared modulus is proportional to the beam density, that is obtained in the Hartree's mean field approximation, after disregarding the exchange interactions. The analysis of this pair of equations, which in general exhibits a strong nonlocal character, is carried out analytically as well as numerically in both the linear and the nonlinear regimes, showing the existence of the quantum beam vortices in the form of Laguerre-Gauss modes and ring envelope solitons, respectively. In particular, when the relation between the plasma wake field response and the beam probability density is strictly local, the pair of the governing equations is reduced to the 2D Gross-Pitaevskii equation that allows one to establish the conditions for the self focusing and collapse. These conditions include the quantum nature of the beam particles. Finally, when the relation between the plasma wake field response and the beam probability density is moderately nonlocal, the above pair of equations permits to follow the spatio-temporal evolution of a quantum ring envelope soliton. Such a structure exhibits small or violent breathing, but it remains very stable for long time.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2013

Plasma turbulence in the scrape-off layer of tokamak devices

Plasma turbulence is explored in the scrape-off layer of tokamak devices using three-dimensional global two-fluid simulations. Two transport regimes are discussed: one in which the turbulent fluctuations saturate nonlinearly due to the Kelvin-Helmholtz instability, and another in which the fluctuations saturate due to a local flattening of the plasma gradients and associated removal of the linear instability drive. Focusing on the latter regime, analytical estimates of the cross-field transport and plasma profile gradients are obtained that display Bohm-scaling diffusion properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2014

Solitons and shocks in dense astrophysical magnetoplasmas with relativistic degenerate electrons and positrons

The linear and nonlinear properties of the ion-acoustic (IA) waves are investigated in a relativistically degenerate magnetoplasma, whose constituents are the electrons, positrons, and ions. The electrons and positrons are assumed to obey the Fermi-Dirac statistics, whereas the cold ions are taken to be inertial and magnetized. In linear analysis, various limiting cases are discussed both analytically and numerically. However, for nonlinear studies, the well-known reductive perturbation technique is employed to derive the Zakharov-Kuznetsov and Zakharov-Kuznetsov Burgers equations in the presence of relativistically degenerate electrons and positrons. Furthermore, with the use of hyperbolic tangent method, the equations are simplified to admit the soliton and shock wave solutions. Numerically, it is shown that the amplitude, width, and phase speed associated with the localized IA solitons and shocks are significantly influenced by the various intrinsic plasma parameters relevant to our model. The present analysis can be useful for understanding the collective processes in dense astrophysical environments like neutron stars, where the electrons and positrons are expected to be relativistic and degenerate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Structural transition of vortices to nonlinear regimes in a dusty plasma

The structural transition of a steady state dust flow from linear to nonlinear regimes is analyzed using a two-dimensional hydrodynamic model for the dust fluid confined in an axisymmetric toroidal system along with an unbounded streaming plasma. Numerical solutions of the employed hydrodynamical model not only confirms the analytical structure of the driven dust vortex flow in the linear limit as reported in the previous analysis but also shows how the dust vortices are strongly affected by the nonlinear convective transport of the flow at the higher Reynolds number (Re) regime. Effects of various system parameters including external driving field and the Reynolds number are investigated within the linear to nonlinear transition regime 0.001 ≤ Re < 50. In agreement with relevant experimental observations, the steady flow structure which is symmetric around the center in the linear regime begins to turn asymmetric in the nonlinear regime. The structure of the steady dust flow is found to be influenced mainly by the dissipation scales due to kinematic viscosity, ion drag, and neutral collision in the nonlinear regime, whereas, in the linear regime, it is mainly controlled by the external driving field and the confining boundaries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Extensions of a classical mechanics “piston-model” for understanding the impact of asymmetry on ICF implosions: The cases of mode 2, mode 2/1 coupling, time-dependent asymmetry, and the relationship to coast-time

As long suspected, low mode asymmetry in inertially confined fusion (ICF) implosions has been implicated as a performance limiting factor [Casey et al., “Evidence of three-dimensional asymmetries seeded by high-density carbon-ablator nonuniformity in experiments at the national ignition facility,” Phys. Rev. Lett. 126, 025002 (2021)]. Recently a non-linear, but solvable, theory [Hurricane et al., “An analytic asymmetric-piston model for the impact of mode-1 shell asymmetry on ICF implosions,” Phys. Plasmas 27, 062704 (2020)] based upon the simple picture of a pair of asymmetric pistons has generated new insights and provided some practical formulas for estimating the degradation of an implosion due to mode-1 asymmetry and demonstrated a previously unrecognized connection between measured hot-spot drift velocity, nuclear down-scatter ratio asymmetry, and the concept of residual kinetic energy (RKE). Asymmetry of the implosion “shell,” as opposed to asymmetry of the hot-spot, was key to the classical mechanics model because the majority of the kinetic energy in an implosion is carried by the shell. Herein, the two-piston model is extended to a six-piston model in order to capture mode-2 asymmetry and coupling between mode-1 and mode-2. A key result of this new six-piston model is that the weighted harmonic mean of shell areal density is the fundamental quantity that determines the RKE and performance degradations for a three-dimensional implosion. Agreement is found between the scalings coming from the theory and ICF implosion data from the National Ignition Facility and to large ensembles of detailed simulations. The connection between the piston model's dependence upon the radius of peak velocity and coast-time is also highlighted in this paper. Finally, by extending the two-piston model to include time-dependent “swing,” it is shown in the Appendix that the shell asymmetry at the time of stagnation dominates the solution for RKE.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Laser polarization effects on crossed-beam energy transfer in inertial confinement fusion

Crossed-beam energy transfer (CBET) is a consequential process in inertial confinement fusion (ICF) experiments. CBET depends on the polarization state of the interacting lasers and can, in turn, alter their polarization. Here, we derive analytical expressions for two-beam CBET with linearly and circularly polarized light, and present simulations of CBET that include polarization effects for ICF conditions relevant to experiments on the National Ignition Facility. The results show that CBET mixes the polarization of the beams as they propagate through the target and leads to azimuthal power imbalances between beams within a given cone (i.e., at the same polar angle in the target chamber). These variations are shown to correlate with variations in measured backscatter between beams of a same quadruplet. Using circularly polarized, instead of linearly polarized, light produces similar overall levels of CBET within a cone of beams but tends to reduce the azimuthal variations. This is expected to slightly improve irradiation symmetry and reduce the risk of backscatter from stimulated Brillouin scattering. Circular polarization may therefore be beneficial for the next generation of laser fusion drivers.

Physics - Plasma physics↗

DOE OSTI2026

Machine Learning–Augmented Laser-Induced Breakdown Spectroscopy for Spectral Discrimination of Iron Oxalates

Enhanced characterization and phase identification of post-PUREX Pu Oxalates (PuOXA) are pivotal for nonproliferation and pre-detonation nuclear forensics. Despite significant advances in the characterization of PuO 2 samples, little is known about the impact of both the chemical structure and oxidation states of PuOXA (i.e., Pu(III) and Pu(IV)) have on optical emission signatures. Here, we demonstrate the analytical capabilities of laser-induced breakdown spectroscopy (LIBS) applied to Fe(II) and Fe(III) oxalate samples as surrogates for PuOXA, highlighting the discriminating features in the LIBS emission spectra arising from differences in the oxidation states within mixed FeOXA samples. We report the enhancement of spectral feature selection using Principal Component Analysis (PCA), which enables the analytical superiority of machine learning algorithms such as Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA), Partial Least Squares Regression (PLSR), Support Vector Regression (SVR), and Random Forest Regression (RFR) over conventional univariate techniques for phase discrimination and chemometric analysis. Cluster analysis revealed how both matrix effects and laser ablation influence cluster separability by introducing spectral artifacts that misdirect the maximization of variance. PCA-selected emission lines were used in the regression models, demonstrating that both univariate and multivariate linear regression models (i.e., PLSR and SVR) can achieve acceptable performance, with machine learning models outperforming conventional calibration regressions. Furthermore, the application of non-linearly activated PCA-selected emission lines illustrates how simplifying the data while retaining captured variance enables the use of less complex and more computationally efficient models. Furthermore, this is particularly evident in the underperformance of RFR, which suffers from increased computational costs and overfitting owing to its high complexity.

Oxalates↗

DOE OSTI2014

Perpendicular diffusion of energetic particles in noisy reduced magnetohydrodynamic turbulence

A model for noisy reduced magnetohydrodynamic turbulence was recently proposed. This model was already used to study the random walk of magnetic field lines. In the current article we use the same model to investigate the diffusion of energetic particles across the mean magnetic field. To compute the perpendicular diffusion coefficient, two analytical theories are used, namely, the Non-Linear Guiding Center theory and the Unified Non-Linear Transport (UNLT) theory. It is shown that the two theories provide different results for the perpendicular diffusion coefficient. We also perform test-particle simulations for the aforementioned turbulence model. We show that only the UNLT theory describes perpendicular transport accurately, confirming that this is a powerful tool in diffusion theory.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

SELF-GRAVITATIONAL FORCE CALCULATION OF SECOND-ORDER ACCURACY FOR INFINITESIMALLY THIN GASEOUS DISKS IN POLAR COORDINATES

Investigating the evolution of disk galaxies and the dynamics of proto-stellar disks can involve the use of both a hydrodynamical and a Poisson solver. These systems are usually approximated as infinitesimally thin disks using two-dimensional Cartesian or polar coordinates. In Cartesian coordinates, the calculations of the hydrodynamics and self-gravitational forces are relatively straightforward for attaining second-order accuracy. However, in polar coordinates, a second-order calculation of self-gravitational forces is required for matching the second-order accuracy of hydrodynamical schemes. We present a direct algorithm for calculating self-gravitational forces with second-order accuracy without artificial boundary conditions. The Poisson integral in polar coordinates is expressed in a convolution form and the corresponding numerical complexity is nearly linear using a fast Fourier transform. Examples with analytic solutions are used to verify that the truncated error of this algorithm is of second order. The kernel integral around the singularity is applied to modify the particle method. The use of a softening length is avoided and the accuracy of the particle method is significantly improved.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Alpha Air Sample Counting Efficiency Versus Dust Loading: Evaluation of a Large Data Set

Dust loading on air sample filters is known to cause a loss of efficiency for direct counting of alpha activity on the filters, but the amount of dust loading and the correction factor needed to account for attenuated alpha particles is difficult to assess. In this paper, correction factors are developed by statistical analysis of a large database of air sample results for a uranium and plutonium processing facility at the Savannah River Site. As is typically the case, dust-loading data is not directly available, but sample volume is found to be a reasonable proxy measure; the amount of dust loading is inferred by a combination of the derived correction factors and a Monte Carlo model. The technique compares the distribution of activity ratios [beta/(beta + alpha)] by volume and applies a range of correction factors on the raw alpha count rate. The best-fit results with this method are compared with MCNP modeling of activity uniformly deposited in the dust and analytical laboratory results of digested filters. Finally, a linear fit is proposed to evenly-deposited alpha activity collected on filters with dust loading over a range of about 2 mg cm -2 to 1,000 mg cm -2 .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗