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At least 271 records · Page 15

Residue Specific Characterization of Electrostatics, Conformational Heterogeneity, and Dynamics of Electron Transfer Proteins with Linear and Nonlinear Infrared Spectroscopy. Final Report

The goal of this research project was to further our understanding of biological electron transfer through the development and application of new methods for studying proteins and their complexes with high spatial and temporal detail. The approach was based on incorporation of reporter bonds with distinct vibrational frequencies at specific locations in proteins and their characterization through the interaction of the bonds with pulses of infrared light. The project focused on the proteins plastocyanin (Pc) and cytochrome (cyt) f, two electron transfer partners in photosynthesis. The first thrust of the project was the incorporation of carbon deuterium bonds as non-perturbative probes at a ligand to the copper ion of Pc and their use to detect changes in the bonding due to the number of electrons at the metal and how the bonding changes upon association with cyt f. Toward developing more advanced approaches to characterize proteins, we incorporated a stronger reporter, the cyano group of cyanophenylalanine, at several locations in Pc and measured the frequency dynamics in the absence and presence of cyt f. The acquired data improved the current model for the protein complex. Notably, the data indicated that the majority of the population is involved in a loosely bound complex, providing insight into the nature of the ensembles formed by electron transfer protein complexes that is not available via other approaches. In addition to learning about the protein complex, we made strides toward developing and improving the new experimental approach to study highly dynamic behaviors of proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Gelation and Re-entrance in Mixtures of Soft Colloids and Linear Polymers of Equal Size

Liquid mixtures composed of colloidal particles and much smaller non-adsorbing linear homopolymers can undergo a gelation transition due to polymer-mediated depletion forces. We now show that the addition of linear polymers to suspensions of soft colloids having the same hydrodynamic size yields a liquid-togel-to-re-entrant liquid transition. In particular, the dynamic state diagram of 1,4-polybutadiene star-linear polymer mixtures was determined with the help of linear viscoelastic and small-angle Xray scattering experiments. While keeping the star polymers below their nominal overlap concentration, a gel was formed upon increasing the linear polymer content. Further addition of linear chains yielded a re-entrant liquid. This unexpected behavior was rationalized by the interplay of three possible phenomena: (i) depletion interactions, driven by the size disparity between the stars and the polymer length scale which is the mesh size of its entanglement network; (ii) colloidal deswelling due to the increased osmotic pressure exerted onto the stars; and (iii) a concomitant progressive suppression of the depletion efficiency on increasing the polymer concentration due to reduced mesh size, hence a smaller range of attraction. Our results unveil an exciting new way to tailor the flow of soft colloids and highlight a largely unexplored path to engineer soft colloidal mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-consistent interaction of linear gravitational and electromagnetic waves in non-magnetized plasma

Here, this paper explores the hybridization of linear metric perturbations with linear electromagnetic (EM) perturbations in non-magnetized plasma for a general background metric. The local wave properties are derived from first principles for inhomogeneous plasma, without assuming any symmetries of the background metric. First, we derive the effective (“oscillation-center”) Hamiltonian that governs the average dynamics of plasma particles in a prescribed quasimonochromatic wave that involves metric perturbations and EM fields simultaneously. Then, using this Hamiltonian, we derive the backreaction of plasma particles on the wave itself and obtain gauge-invariant equations that describe the resulting self-consistent gravito-electromagnetic (GEM) waves in a plasma. The transverse tensor modes of gravitational waves are found to have no interaction with the plasma and the EM modes in the geometrical-optics limit. However, for $longitudinal$ GEM modes with large values of the refraction index, the interplay between gravitational and EM interactions in plasma can have a strong effect. In particular, the dispersion relation of the Jeans mode is significantly affected by electrostatic interactions. As a spin-off, our calculation also provides an alternative resolution of the so-called Jeans swindle.

79 ASTRONOMY AND ASTROPHYSICS↗

Compensating slice emittance growth in high brightness photoinjectors using sacrificial charge

Achieving maximum electron beam brightness in photoinjectors requires detailed control of the 3D bunch shape and precise tuning of the beam focusing. Even in state-of-the-art designs, slice emittance growth due to nonlinear space charge forces and partial nonlaminarity often remains non-negligible. In this work, we introduce a new means to linearize the transverse slice phase space: a sacrificial portion of the bunch’s own charge distribution, formed into a wavebroken shock front by highly nonlinear space charge forces within the gun, whose downstream purpose is to dynamically linearize the desired bunch core. We show that linearization of an appropriately prepared bunch can be achieved via strongly nonlaminar focusing of the sacrificial shock front, while the inner core focuses laminarly. This leads to a natural spatial separation of the two distributions: a dense core surrounded by a diffuse halo of sacrificial charge that can be collimated. Multiobjective genetic algorithm optimizations of the ultracompact x-ray free electron laser injector employ this concept, and we interpret it with an analytic model that agrees well with the simulations. In simulation, we demonstrate a final bunch charge of 100 pC, peak current ∼ 30 A, and a sacrificial charge of 150 pC (250 pC total emitted from cathode) with normalized emittance growth of < 20 nm rad due to space charge. This implies a maximum achievable brightness approximately an order of magnitude greater than existing free electron laser injector designs. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

Scorpius and The Integrated Test Stand [Slides]

Scorpius will provide (DARHT scale) flash-radiography of dynamic nuclear material. DARHT radiographs non-nuclear (surrogate) materials at a cadence of 8 to 10 hydrodynamic shots per year. Scorpius will radiograph nuclear material at an initial cadence of about 2 to 3 subcritical shots per year in a more challenging environment. Both machines are Linear Induction Accelerators (LIAs) and generate X-rays with high-current, relativistic electron beams. Their use is termed Flash-Radiography.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Model and remote-sensing-guided experimental design and hypothesis generation for monitoring snow-soil–plant interactions

In this study, we develop a machine-learning (ML)-enabled strategy for selecting hillslope-scale ecohydrological monitoring sites within snow-dominated mountainous watersheds, with a particular focus on snow-soil–plant interactions. Data layers rely on spatial data layers from both remote sensing and hydrological model simulations. Specifically, a Landsat-based foresummer drought sensitivity index is used to define the dependency of the annual peak plant productivity on the Palmer drought severity index in the early growing season. Hydrological simulations provide the spatiotemporal dynamics of near-surface soil moisture and snow depth. In this framework, a regression analysis identifies the key hydrological variables relevant to the spatial heterogeneity of drought sensitivity. We then apply unsupervised clustering to these key variables, using the Gaussian mixture model, to group hillslopes into several zones that have divergent relationships regarding soil moisture, snow dynamics, and drought sensitivity. Using the datasets collected in the East River Watershed (Crested Butte, Colorado, United States), results show that drought sensitivity is significantly correlated with model-derived soil moisture and snow-free timing over space and time. The relationship is, however, non-linear, such that the correlation decreases above a threshold elevation and in a heavy snow year due to large snowpacks, lateral flow, and soil storage limitations. Clustering is then able to define the zones that have high or low sensitivity to drought, as well as the mid-elevation regions where sensitivity is associated with the topographic aspect and net potential radiation. In addition, the algorithm identifies the most representative hillslopes with road/trail access within each zone for installing monitoring sites. Our method also aims to significantly increase the use of ML and model-simulation results to guide critical zone and watershed monitoring activities.

54 ENVIRONMENTAL SCIENCES↗

QLBT: a linear Boltzmann transport model for heavy quarks in a quark-gluon plasma of quasi-particles

Abstract We develop a new heavy quark transport model, QLBT, to simulate the dynamical propagation of heavy quarks inside the quark-gluon plasma (QGP) created in relativistic heavy-ion collisions. Our QLBT model is based on the linear Boltzmann transport (LBT) model with the ideal QGP replaced by a collection of quasi-particles to account for the non-perturbative interactions among quarks and gluons of the hot QGP. The thermal masses of quasi-particles are fitted to the equation of state from lattice QCD simulations using the Bayesian statistical analysis method. Combining QLBT with our advanced hybrid fragmentation-coalescence hadronization approach, we calculate the nuclear modification factor $$R_\mathrm {AA}$$ R AA and the elliptic flow $$v_2$$ v 2 of D mesons at the Relativistic Heavy-Ion Collider and the Large Hadron Collider. By comparing our QLBT calculation to the experimental data on the D meson $$R_\mathrm {AA}$$ R AA and $$v_2$$ v 2 , we extract the heavy quark transport parameter $$\hat{q}$$ q ^ and diffusion coefficient $$D_\mathrm {s}$$ D s in the temperature range of $$1-4~T_\mathrm {c}$$ 1 - 4 T c , and compare them with the lattice QCD results and other phenomenological studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Variance Reduction within Implicit Monte Carlo Thermal Radiation Transport using the Local Importance Function Transform [Slides]

System of equations derived by Fleck and Cummings to model time-dependent thermal radiative transfer (TRT) problems: Solution of radiation specific intensity (I), non-linearly coupled to material internal energy (U); Absorption and re-emission approximated by effective scattering events. Useful for high-energy density physics simulations: i.e., astrophysics, inertial confinement fusion (ICF). Whereas deterministic methods are fully discretized and free of statistical noise, Monte Carlo methods allow for dynamic sampling of the phase space at the price of statistical noise; Monte Carlo methods are also characterized by a slow $\frac{1}{√Ν}$ convergence rate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Analytical integration of the tractions induced by non-singular dislocations on an arbitrary shaped triangular quadratic element

Here, an analytical model is proposed to evaluate the nodal force induced by a segment of dislocation upon an arbitrary shaped triangular element. This calculation is required in hybrid methods that associate dislocation dynamics to boundary or finite element to solve simultaneously the evolution of large ensembles of dislocations with complex boundary conditions. Nodal forces are defined as the triple integration of the unbalanced traction field induced by a straight dislocation upon the surface of the element. Following our previous approach (Queyreau et al 2014 Modelling Simul. Mater. Sci. Eng. 22 035004) on a simpler geometry and in the case of linear isotropic elasticity, triple integrals are solved by sequences of integration by parts that exhibit recurrence relations. The traction field is defined and finite everywhere even at the core of dislocations, thanks to the use of the non-singular stress expression formulated by Cai et al (2006 J. Mech. Phys. Solids 54 561–587). The nodal force expressions can be used when considering both a single convolution or double convolution of the Green's function with the core distribution. A solution is also proposed for the case of a semi-infinite segment through the study of the asymptotic behavior of the analytical expressions. The proposed approach is exact and very computationally efficient. The choice of an arbitrary shaped triangular element and quadratic shape functions allow the consideration of complex geometries and comply with automatic meshing procedures. These analytical expressions could also be employed to estimate dislocation interactions with interfaces.

42 ENGINEERING↗

Potential Non-Linearities in the High Latitude Circulation and Ozone Response to Stratospheric Aerosol Injection

The impacts of Stratospheric Aerosol Injection (SAI) on the atmosphere and surface climate depend on when and where the sulfate aerosol precursors are injected, as well as on how much surface cooling is to be achieved. We use a set of CESM2(WACCM6) SAI simulations achieving three different levels of global mean surface cooling and demonstrate that unlike some direct surface climate impacts driven by the reflection of solar radiation by sulfate aerosols, the SAI-induced changes in the high latitude circulation and ozone are more complex and could be non-linear. This manifests in our simulations by disproportionally larger Antarctic springtime ozone loss, significantly larger intra-ensemble spread of the Arctic stratospheric jet and ozone responses, and non-linear impacts on the extratropical modes of surface climate variability under the strongest-cooling SAI scenario compared to the weakest one. These potential non-linearities may add to uncertainties in projections of regional surface impacts under SAI.

54 ENVIRONMENTAL SCIENCES↗

Focused wave interactions with floating structures: a blind comparative study

The paper presents results from the Collaborative Computational Project in Wave Structure Interaction (CCP-WSI) Blind Test Series 2. Without prior access to the physical data, participants, with numerical methods ranging from low-fidelity linear models to fully non-linear Navier-Stokes (NS) solvers, simulate the interaction between focused wave events and two separate, taut-moored, floating structures: a hemispherical-bottomed cylinder and a cylinder with a moonpool. The ‘blind’ numerical predictions for heave, surge, pitch and mooring load, are compared against physical measurements. Dynamic time warping is used to quantify the predictive capability of participating methods. In general, NS solvers and hybrid methods give more accurate predictions; however, heave amplitude is predicted reasonably well by all methods; and a WEC-Sim implementation, with CFD-informed viscous terms, demonstrates comparable predictive capability to even the stronger NS solvers. Large variations in the solutions are observed (even among similar methods), highlighting a need for standardisation in the numerical modelling of WSI problems.

42 ENGINEERING↗

Transition Zones at the Changing Coastal Terrestrial‐Aquatic Interface

Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience spatial and temporal variability in biogeochemical processes, driven by marsh‐to‐upland gradients and hydrological fluctuations. These fluctuations make it difficult to understand and predict biogeochemical processes in these highly dynamic systems. We studied coastal soil biogeochemistry and its variability (a) at regional scales and (b) across transects from upland forest to marsh, in two contrasting regions—Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity‐related analytes were a key source of variability in soil biogeochemistry, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI—however, contrary to expectations, transition soils were not consistently intermediate between upland and marsh endmembers; the non‐monotonic trends of C, P, Fe along our transects suggest that these do not behave as expected and may be difficult to model and predict—thus these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients (e.g., Ca, K, CEC, and TS) may act as precursors to ecosystem shifts. Our comprehensive soil characterization represents a snapshot of a single timepoint of surface soils and provides essential data for mechanistic modeling of ecosystem dynamics across coastal transects.

Patel, Kaizad F. [Pacific Northwest National Labor↗

The inviscid incompressible limit of Kelvin–Helmholtz instability for plasmas

The Kelvin–Helmholtz Instability (KHI) is an interface instability that develops between two fluids or plasmas flowing with a common shear layer. KHI occurs in astrophysical jets, solar atmosphere, solar flows, cometary tails, planetary magnetospheres. Two applications of interest, encompassing both space and fusion applications, drive this study: KHI formation at the outer flanks of the Earth’s magnetosphere and KHI growth from non-uniform laser heating in magnetized direct-drive implosion experiments. Here, we study 2D KHI with or without a magnetic field parallel to the flow. We use both the GAMERA code, which solves the compressible Euler equations, and the STRATOSPEC code, which solves the Navier-Stokes equations under the Boussinesq approximation, coupled with the magnetic field dynamics. GAMERA is a global three-dimensional MHD code with high-order reconstruction in arbitrary nonorthogonal curvilinear coordinates, which is developed for a large range of astrophysical applications. STRATOSPEC is a three-dimensional pseudo-spectral code with an accuracy of infinite order (no numerical diffusion). Magnetized KHI is a canonical case for benchmarking hydrocode simulations with extended MHD options. An objective is to assess whether or not, and under which conditions, the incompressibility hypothesis allows to describe a dynamic compressible system. For comparing both codes, we reach the inviscid incompressible regime, by decreasing the Mach number in GAMERA, and viscosity and diffusion in STRATOSPEC. Here, we specifically investigate both single-mode and multi-mode initial perturbations, either with or without magnetic field parallel to the flow. The method relies on comparisons of the density fields, 1D profiles of physical quantities averaged along the flow direction, and scale-by-scale spectral densities. We also address the triggering, formation and damping of filamentary structures under varying Mach number or Atwood number, with or without a parallel magnetic field. Comparisons show very satisfactory results between the two codes. The vortices dynamics is well reproduced, along with the breaking or damping of small-scale structures. We end with the extraction of growth rates of magnetized KHI from the compressible regime to the incompressible limit in the linear regime assessing the effects of compressibility under increasing magnetic field. The observed differences between the two codes are explained either from diffusion or non-Boussinesq effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NaGaS 2 : An Elusive Layered Compound with Dynamic Water Absorption and Wide‐Ranging Ion‐Exchange Properties

Abstract Most ternary sulfides belonging to the MGaS 2 structure‐type have been known for many years and are well‐characterized. Surprisingly, there have been no reports of the NaGaS 2 composition, which contains Na, a monovalent cation slightly larger in size than Li, found in LiGaS 2 , a compound known for its non‐linear optical properties. Now it is demonstrated for the first time that the unique reversible water absorption in NaGaS 2 has resulted in its absence from previous reports owing to difficulties encountered when characterizing this compound by SC XRD. The layered structure of this compound coupled with uniquely easy migration of water molecules between the layers allows for ion exchange with 3d and 5f metal cations. Some cations, for example, Ni 2+ , facilitate exfoliation of the layers, providing a facile synthetic route to a new class of 2D chalcogenide materials and furthermore demonstrating that NaGaS 2 can readily uptake uranyl species from aqueous solutions.

Klepov, Vladislav V.↗

Combining 3-Momentum and Kinetic Energy on Galilei/Newton Spacetime

Without the mass-energy equivalence available on Minkowski spacetime M, it is not possible on 4-dimensional non-relativistic Galilei/Newton spacetime G to combine 3-momentum and total mass-energy in a single tensor object. However, given a fiducial frame, it is possible to combine 3-momentum and kinetic energy into a linear form (particle) or (1,1) tensor (continuum) in a manner that exhibits increased unity of classical mechanics on flat relativistic and non-relativistic spacetimes M and G. As on M, for a material continuum on G, the first law of thermodynamics can be considered a consequence of a unified dynamical law for energy-momentum rather than an independent postulate.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Linear and nonlinear viscoelasticity of concentrated thermoresponsive microgel suspensions

We present an integrated experimental and theoretical study of the dynamics and rheology of self-crosslinked, slightly charged, temperature responsive soft poly(N-isopropylacrylamide) (pNIPAM) microgels over a wide range of concentration and temperature spanning the sharp change in particle size and intermolecular interactions across the lower critical solution temperature (LCST). Dramatic, non-monotonic changes in viscoelasticity are observed as a function of temperature, with distinct concentration dependence in the dense fluid, glassy, and soft-jammed regimes. Motivated by our experimental observations, we formulate a minimalistic model for the size dependence of a single microgel particle and the change of the interparticle interaction from purely repulsive to attractive upon heating. Using microscopic equilibrium and time-dependent statistical mechanical theories, theoretical predictions are quantitatively compared with experimental measurements of the shear modulus. Good agreement is found for the nonmonotonic temperature behavior that originates as a consequence of the competition between reduced microgel packing fraction and increasing interparticle attractions. Furthermore, testable predictions are made for nonlinear rheological properties such as the yield stress and strain. To our knowledge, this is the first attempt to quantitatively understand in a unified manner the viscoelasticity of dense, temperature-responsive microgel suspensions spanning a wide range of temperatures and concentrations.

42 ENGINEERING↗

Influence of alloy solidification path on melt pool behavior in additive manufacturing

Numerical models used to study transport phenomena in laser-powder bed fusion processes often rely on assumptions and simplifications to reduce their computational expense. One common simplification is in the description of latent heat evolution during the solid-liquid phase change (i.e., the solidification pathway), justified by the fact that the mushy zone thickness is similar to the numerical grid spacing used for continuum transport models. The lack of resolution of transport phenomena in the mushy zone motivates the use of computationally convenient solidification paths such as linear or sigmoidal relationships over pathways derived from fundamental solidification theory such as equilibrium or Scheil models. In the present work, an uncertainty quantification (UQ) framework is used to analyze the influence of solidification pathway selection on the solidification dynamics and melt pool geometries in laser based additive manufacturing (AM) of IN625. Results show the solidification pathway has a quantifiable influence on the cooling rate at the liquidus isotherm, mushy zone thickness, and solidification time. Due to similarities in the latent heat evolution at the beginning of solidification, the equilibrium and Scheil models predict similar cooling rates near the liquidus isotherm, however the wider freezing range of Scheil leads to a wider mushy zone compared to equilibrium. The non-physical latent heat release profiles of sigmoidal and linear paths lead to significant overpredictions of cooling rates at the liquidus isotherm compared to equilibrium and Scheil. Finally, these results indicate that careful consideration should be given to the choice of solidification pathway to ensure reliable model predictions.

36 MATERIALS SCIENCE↗