Protein cage assembly across multiple length scales
Assembly of protein cages across multiple length scales is described, with an emphasis on their use as functional biomaterials.
Chemistry↗
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Multi-scale chemo-mechanical evolution during crystallization of mixed conducting SrTi[subscript 0.6
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Buckner, Haley B.↗
Scale tests of the new DUNE data pipeline
In preparation for the second runs of the ProtoDUNE detectors at CERN (NP02 and NP04)[1], DUNE has established a new data pipeline for bringing the data from the EHN-1 experimental hall at CERN to primary tape storage at Fermilab and CERN, and then spreading it out to a distributed disk data store at many locations around the world. This system includes a new Ingest Daemon and a new Declaration Daemon. The Rucio[2] replica catalog, and FTS3 transport are used to transport all files. All file metadata is declared to the new MetaCat[3] metadata service. All of these new components have been successfully tested at a scale equal to the expected output of the detector data acquisition system (~2-4 GB/s), and the expected network bandwidth out of the experimental hall. We present the procedure that was used to test and the results of the test.
Timm, Steven↗
Small scale coherent vortex generation in drift wave-zonal flow turbulence
We present a paradigm for the generation of small scale coherent vortex (SSCV) in drift wave-zonal flow (DW-ZF) turbulence. We demonstrate that phases of DWs can couple coherently, mediated by the ZF shearing. A SSCV is formed when the phases of the DWs are “attracted” to form a stable “phase cluster.” We show that the ZF shearing induces asymmetry between “attractive” and “repulsive” phase couplings, so that a net attractive phase coupling results. The turbulent DWs will (partially)synchronize into a stable SSCV at locations, where the attractive phase coupling induced by the ZF shearing exceeds the “detuning” effects by the DW dispersion and random phase scattering. We also discuss the “self-binding” effect of the newly formed SSCV.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Scaling magnetized liner inertial fusion on Z and future pulsed-power accelerators
The MagLIF (Magnetized Liner Inertial Fusion) concept [S. A. Slutz et al., Phys. Plasmas 17, 056303 (2010)] has demonstrated fusion–relevant plasma conditions [M. R. Gomez et al., Phys. Rev. Lett. 113, 155003 (2014)] on the Z accelerator with a peak drive current of about 18 MA. We present 2D numerical simulations of the scaling of MagLIF on Z as a function of drive current, preheat energy, and applied magnetic field. The results indicate that deuterium-tritium (DT) fusion yields greater than 100 kJ could be possible on Z when all of these parameters are at the optimum values: i.e., peak current = 25 MA, deposited preheat energy = 5 kJ, and B{sub z} = 30 T. Much higher yields have been predicted [S. A. Slutz and R. A. Vesey, Phys. Rev. Lett. 108, 025003 (2012)] for MagLIF driven with larger peak currents. Two high performance pulsed-power accelerators (Z300 and Z800) based on linear-transformer-driver technology have been designed [W. A. Stygar et al., Phys. Rev. ST Accel. Beams 18, 110401 (2015)]. The Z300 design would provide 48 MA to a MagLIF load, while Z800 would provide 65 MA. Parameterized Thevenin-equivalent circuits were used to drive a series of 1D and 2D numerical MagLIF simulations with currents ranging from what Z can deliver now to what could be achieved by these conceptual future pulsed-power accelerators. 2D simulations of simple MagLIF targets containing just gaseous DT have yields of 18 MJ for Z300 and 440 MJ for Z800. The 2D simulated yield for Z800 is increased to 7 GJ by adding a layer of frozen DT ice to the inside of the liner.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory
Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still two important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling “partially contracted” NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient “electron pair prescreening” that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed comparison between the partial and strong contraction schemes is made, with conclusions that discourage the strong contraction scheme as a basis for local correlation methods due to its non-invariance with respect to rotations in the inactive and external subspaces. A minimal set of conservatively chosen truncation thresholds controls the accuracy of the method. With the default thresholds, about 99.9% of the canonical partially contracted NEVPT2 correlation energy is recovered while the crossover of the computational cost with the already very efficient canonical method occurs reasonably early; in linear chain type compounds at a chain length of around 80 atoms. Calculations are reported for systems with more than 300 atoms and 5400 basis functions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys
Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material’s structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of material defects, and we compare the material behavior displayed with expectations from experiment and theory. We also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Determination of crystal growth rates during rapid solidification of polycrystalline aluminum by nano-scale spatio-temporal resolution in situ transmission electron microscopy
In situ investigations of rapid solidification in polycrystalline Al thin films were conducted using nano-scale spatio-temporal resolution dynamic transmission electron microscopy. Differences in crystal growth rates and asymmetries in melt pool development were observed as the heat extraction geometry was varied by controlling the proximity of the laser-pulse irradiation and the associated induced melt pools to the edge of the transmission electron microscopy support grid, which acts as a large heat sink. Experimental parameters have been established to maximize the reproducibility of the material response to the laser-pulse-related heating and to ensure that observations of the dynamical behavior of the metal are free from artifacts, leading to accurate interpretations and quantifiable measurements with improved precision. Interface migration rate measurements revealed solidification velocities that increased consistently from ∼1.3 m s{sup −1} to ∼2.5 m s{sup −1} during the rapid solidification process of the Al thin films. Under the influence of an additional large heat sink, increased crystal growth rates as high as 3.3 m s{sup −1} have been measured. The in situ experiments also provided evidence for development of a partially melted, two-phase region prior to the onset of rapid solidification facilitated crystal growth. Using the experimental observations and associated measurements as benchmarks, finite-element modeling based calculations of the melt pool evolution after pulsed laser irradiation have been performed to obtain estimates of the temperature evolution in the thin films.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Atomic scale study of surface orientations and energies of Ti 2 O 3 crystals
For nanostructured particles, the faceting planes and their terminating chemical species are two critical factors that govern their chemical behavior. In this paper, the surface atomistic structure and termination of Ti 2 O 3 crystals were analyzed using atomic-scale aberration-corrected scanning transmission electron microscopy (STEM) combined with density functional theory (DFT) calculations. STEM imaging reveals that the Ti 2 O 3 crystals are most often faceted along (001), (012), (-114), and (1–20) planes. The DFT calculation indicates that the (012) surface with TiO-termination has the lowest cleavage energy and correspondingly the lowest surface energy, indicating that (012) will be the most stable and prevalent surfaces in Ti 2 O 3 nanocrystals. Finally, these observations provide insights for exploring the interfacial process involving Ti 2 O 3 nanoparticles.
36 MATERIALS SCIENCE↗
Examining astrophysical gas cloud collapse using an optical depth-scaled, x-ray-irradiated, carbon-foam sphere
When stellar radiation interacts with a molecular cloud, the cloud's fate depends on the strength of the incident radiation and the radiation's mean-free-path within the cloud [F. Bertoldi, Astrophys. J. 346, 735–755 (1989)]. Under the right conditions, the radiation compresses the cloud and a star formation may occur. Where and when the stellar formation occurs in the cloud's collapse are open questions. Direct observation of the complete star–cloud lifecycle is nearly impossible due to the immense timescales and distances over which the interaction occurs. Laboratory astrophysics offers a way to investigate such a system by scaling the important astrophysical parameters to the laboratory. This work describes laboratory experiments to study the radiation-driven implosion of clouds, using x rays from a laser-irradiated, thin, gold foil as a surrogate star and a carbon-foam sphere as a surrogate cloud. An optically thick system, theoretically corresponding to a star-forming regime, was selected by choice of the foam density. Gold foil and sphere motions were imaged by x-ray radiography. Radiographic images show the formation of an interface between rarefied gold and carbon plasmas, a shock moving into the sphere, and a blunting of the initial sphere's shape. Measurements show that the shock moved linearly around 64 μm/ns into the sphere, and the gold–carbon interface formed by 2 ns at the sphere edge remained stationary. The deformation of the sphere was driven by the incident radiation and not by mechanical pressures applied by gold plasma. The blunting of the sphere was likely due to the geometric reduction of flux near the sphere's poles. Higher x-ray flux near the sphere's equator caused high compression and a faster shock, which flattened the sphere. We will discuss the results and implications of our observations.
VanDervort, R. W. [University of Michigan 1 , Ann ↗
Comparing gas composition from fast pyrolysis of live foliage measured in bench-scale and fire-scale experiments
Background: Fire models have used pyrolysis data from oxidising and non-oxidising environments for flaming combustion. In wildland fires pyrolysis, flaming and smouldering combustion typically occur in an oxidising environment (the atmosphere). Aims: Using compositional data analysis methods, determine if the composition of pyrolysis gases measured in non-oxidising and ambient (oxidising) atmospheric conditions were similar. Methods: Permanent gases and tars were measured in a fuel-rich (non-oxidising) environment in a flat flame burner (FFB). Permanent and light hydrocarbon gases were measured for the same fuels heated by a fire flame in ambient atmospheric conditions (oxidising environment). Log-ratio balances of the measured gases common to both environments (CO, CO 2 , CH 4 , H 2 , C 6 H 6 O (phenol), and other gases) were examined by principal components analysis (PCA), canonical discriminant analysis (CDA) and permutational multivariate analysis of variance (PERMANOVA). Key results: Mean composition changed between the non-oxidising and ambient atmosphere samples. PCA showed that flat flame burner (FFB) samples were tightly clustered and distinct from the ambient atmosphere samples. CDA found that the difference between environments was defined by the CO-CO 2 log-ratio balance. PERMANOVA and pairwise comparisons found FFB samples differed from the ambient atmosphere samples which did not differ from each other. Conclusion: Relative composition of these pyrolysis gases differed between the oxidising and non-oxidising environments. This comparison was one of the first comparisons made between bench-scale and field scale pyrolysis measurements using compositional data analysis. Implications: These results indicate the need for more fundamental research on the early time-dependent pyrolysis of vegetation in the presence of oxygen.
54 ENVIRONMENTAL SCIENCES↗
Monitoring of Wind Turbine Gearbox Condition through Oil and Wear Debris Analysis: A Full-Scale Testing Perspective
Despite the wind industry's dramatic development during the past decade, it is still challenged by premature turbine subsystem/component failures, especially for turbines rated above 1 MW. Because a crane is needed for each replacement, gearboxes have been a focal point for improvement in reliability and availability. Condition monitoring (CM) is a technique that can help improve these factors, leading to reduced turbine operation and maintenance costs and, subsequently, lower cost of energy for wind power. Although technical benefits of CM for the wind industry are normally recognized, there is a lack of published information on the advantages and limitations of each CM technique confirmed by objective data from full-scale tests. This article presents first-hand oil and wear debris analysis results obtained through tests that were based on full-scale wind turbine gearboxes rated at 750 kW. The tests were conducted at the 2.5-MW dynamometer test facility at the National Wind Technology Center at the National Renewable Energy Laboratory. The gearboxes were tested in three conditions: run-in, healthy, and damaged. The investigated CM techniques include real-time oil condition and wear debris monitoring, both inline and online sensors, and offline oil sample and wear debris analysis, both onsite and offsite laboratories. The reported results and observations help increase wind industry awareness of the benefits and limitations of oil and debris analysis technologies and highlight the challenges in these technologies and other tribological fields for the Society of Tribologists and Lubrication Engineers and other organizations to help address, leading to extended gearbox service life.
17 WIND ENERGY↗
On the statistics of biased tracers in the Effective Field Theory of Large Scale Structures
With the completion of the Planck mission, in order to continue to gather cosmological information it has become crucial to understand the Large Scale Structures (LSS) of the universe to percent accuracy. The Effective Field Theory of LSS (EFTofLSS) is a novel theoretical framework that aims to develop an analytic understanding of LSS at long distances, where inhomogeneities are small. We further develop the description of biased tracers in the EFTofLSS to account for the effect of baryonic physics and primordial non-Gaussianities, finding that new bias coefficients are required. Then, restricting to dark matter with Gaussian initial conditions, we describe the prediction of the EFTofLSS for the one-loop halo-halo and halo-matter two-point functions, and for the tree-level halo-halo-halo, matter-halo-halo and matter-matter-halo three-point functions. Several new bias coefficients are needed in the EFTofLSS, even though their contribution at a given order can be degenerate and the same parameters contribute to multiple observables. We develop a method to reduce the number of biases to an irreducible basis, and find that, at the order at which we work, seven bias parameters are enough to describe this extremely rich set of statistics. We then compare with the output of an N-body simulation where the normalization parameter of the linear power spectrum is set to σ 8 = 0.9. For the lowest mass bin, we find percent level agreement up to k ≃ 0.3 h Mpc –1 for the one-loop two-point functions, and up to k ≃ 0.15 h Mpc –1 for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. In conclusion, this is consistent with the theoretical estimates, and suggests that the cosmological information in LSS amenable to analytical control is much more than previously believed.
79 ASTRONOMY AND ASTROPHYSICS↗
Lepton number violation as a key to low-scale leptogenesis
We explore the possibility of having a successful leptogenesis through oscillations between new sterile fermion states added to the Standard Model field content in a well motivated framework, naturally giving rise to the required mass splitting between the sterile states through a small total lepton number violation. We propose a framework with only two sterile states forming a pseudo-Dirac state, in which their mass difference as well as the smallness of the neutrino masses are due to two sources of lepton number violation with ΔL=2, corresponding to an Inverse Seesaw framework extended by a Linear Seesaw mass term. We also explore the pure Inverse Seesaw mechanism in its minimal version, requiring at least four new sterile states in order to comply with neutrino data. Our analytical and numerical studies reveal that one can have a successful leptogenesis at the temperature of the electroweak scale through oscillations between the two sterile states with a “natural” origin of the strong degeneracy in their mass spectrum. We also revisit the analytical expression of the baryon asymmetry of the Universe in the weak washout regime of this framework.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Unified no-scale attractors
We have presented previously a general treatment of Starobinsky-like inflation in no-scale supergravity where the tensor-to-scalar ratio r = 3(1–n s ) 2 , and n s is the tilt of the scalar perturbations. In particular, we have shown how this scenario can be unified with modulus fixing, supersymmetry breaking and a small cosmological constant. In this study we extend these constructions to inflationary models based on generalized no-scale structures. In particular, we consider alternative values of the curvature parameter, α < 1, as may occur if not all the complex Kähler moduli contribute to driving inflation, as well as α > 1, as may occur if complex structure moduli also contribute to driving inflation. In all cases, we combine these α-Starobinsky inflation models with supersymmetry breaking and a present-day cosmological constant, allowing for additional contributions to the vacuum energy from stages of gauge symmetry breaking.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Cross-scale interaction between microturbulence and meso-scale reversed shear Alfvén eigenmodes in DIII-D plasmas
Abstract This paper reports global nonlinear gyrokinetic simulations that couple meso-scale reversed shear Alfvén eigenmodes (RSAEs) driven by energetic particles (EPs) and ion temperature gradient (ITG) microturbulence driven by thermal plasma, using equilibrium and profiles from DIII-D discharge #159243. In simulations focusing only on the ITG, electrostatic ITG drives a huge thermal ion heat transport, which is reduced by a factor of 10 to a level close to the experimental value in electromagnetic simulation due to finite β effect. In the simulations coupling the RSAE and ITG, ITG can scatter the resonant EP nonlinearly trapped by the RSAE and damp the zonal flows generated by the RSAE. The regulation of the RSAE by the ITG greatly reduces the initial saturation amplitude of the RSAE but increases the RSAE amplitude and associated EP transport to experimental levels in the quasi-steady state. The RSAE effects on the ITG, specifically the stronger zonal flows generated by the RSAE and the RSAE frequency modulation of the ITG-induced thermal ion heat transport, in turn, leads to a reduction of the thermal ion heat transport by more than a factor of 2 . For a stronger background ITG, the regulation of the RSAE by the ITG is stronger, while the RSAE effects on the ITG are weaker. This work highlights the importance of cross-scale coupling in the dynamics of the AE turbulence and EP transport.
Physics↗
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints
Abstract Background Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models. Results We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions. Availability and implementation Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA Supplementary information Supplementary data are available at Bioinformatics online.
Chan, Siu H. J. (ORCID:000000027707656X)↗
Acoustic scaling of linear and mode-coupled anisotropic flow; implications for precision extraction of the specific shear viscosity
The n th -order linear flow coefficients v n L ( n = 2 , 3 , 4 , 5 ) , and the corresponding nonlinear mode-coupled ( mc ) coefficients v 4 , ( 2 , 2 ) mc , v 5 , ( 2 , 3 ) mc , v 6 , ( 3 , 3 ) mc , and v 6 , ( 2 , 2 , 2 ) mc , are studied for Pb+Pb collisions at s N N = 2.76 TeV. Both sets of coefficients suggest a common acoustic scaling pattern of exponential viscous modulation, with a rate proportional to the square of the harmonic numbers and the mean transverse momenta (respectively), and inversely proportional to the cube root of the charged particle multiplicity [ ( N ch ) 1 / 3 ] , which characterizes the dimensionless size of the systems produced in the collisions. These patterns and their associated scaling parameters offer new stringent constraints for eccentricity-independent estimates of the specific shear viscosity η s ( T ) and the viscous correction to the thermal distribution function for the matter produced in the collisions. They also give crucial constraints for extraction of the initial-state eccentricity spectrum.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗