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At least 19 records

Dirichlet-type absorbing boundary conditions for peridynamic scalar waves in two-dimensional viscous media

Construction of absorbing boundary conditions (ABCs) for nonlocal models is generally challenging, primarily due to the fact that nonlocal operators are commonly associated with volume constrained boundary conditions. Moreover, application of Fourier and Laplace transforms, which are essential for the majority of available methods for ABCs, to nonlocal models is complicated. In this paper, we propose a simple method to construct accurate ABCs for peridynamic scalar wave-type problems in viscous media. The proposed ABCs are constructed in the time and space domains and are of Dirichlet type. Consequently, their implementation is relatively simple, since no derivatives of the wave field are required. The proposed ABCs are derived at the continuum level, from a semi-analytical solution of the exterior domain using harmonic exponential basis functions in space and time (plane-wave modes). The numerical implementation is done using a meshfree collocation approach employed within a boundary layer adjacent to the interior domain boundary. The modes satisfy the peridynamic numerical dispersion relation, resulting in a compatible solution of the interior region (near-field) with that of the exterior region (far-field). The accuracy and stability of the proposed ABCs are demonstrated with several numerical examples in two-dimensional unbounded domains.

42 ENGINEERING↗

Impact experiments in viscous fluid media

Available phase and group velocity data are inverted by a procedure which includes the effects of transverse anisotropy, anelastic dispersion, sphericity, and gravity. The resulting models, for average Earth, average ocean, and oceanic regions divided according to the age of the ocean floor, are quite different from previous results which ignore the above effects. The models show a low-veocity zone with age dependent anisotropy and velocities higher than derived in previous surface wave studied. The correspondence between the anisotropy variation with age and a physical model based on flow aligned olivine is suggestive. For most of the Earth SHSV in the vicinity of the low-velocity zone. Near the East Pacific Rise, however, SVSH at depth, consistent with ascending flow. Anisotropy is as important as temperature in causing radial and lateral variations in velocity. The models have a high velocity nearly isotropic layer at the top of the mantle that thickens with age. This layer defines the LID, or seismic lithosphere. In the Pacific, the LID thickens with age to a maximum thickness of about 50 km. This thickness is comparable to the thickness of the elastic lithosphere. The LID thickness is thinner than derived using isotropic or pseudo-isotropic procedures A new model for Average Earth is obtained which includes a thin LID. This model extends the fit of a P.R.E.M. type model to shorter period surface waves.

Greeley, R.↗

Quantification of Dispersion for Weakly and Strongly Correlated Nanofillers in Polymer Nanocomposites

The dispersion of nanoparticles in viscous polymers is dictated by kinetics, interaction potentials between particles, and interfacial compatibility between the matrix and dispersed phases. It was previously proposed that an analogy can be made between thermally dispersed colloids and kinetically dispersed nanoparticles in viscous media when weak interactions exist between particles allowing for a mean-field description under the Ginzburg criterion such as for carbon black dispersed in polybutadiene elastomer. For these cases, the second virial coefficient can be used to quantify the quality of dispersion; additionally, the nanoscale network mesh size can be calculated, which is related to dynamic properties. However, this approach fails for nanoparticles with surface charges or other specific interactions that lead to correlations. Here, these correlated systems are investigated in the context of the mean-field systems in order to gain a comparative description of dispersion using the network mesh size and a derived virial coefficient. The physical origin of the structural parameters from the proposed model for these correlated systems is investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs

Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT 1 R and CysLT 2 R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing. A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w

97 MATHEMATICS AND COMPUTING↗

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Effect of slow rotational diffusion on angular correlations.

The theory for perturbed angular correlations of gamma radiation has been extended to include the possibility of adiabatic variation in the interaction Hamiltonian, K, for the intermediate state. The calculation begins from a polycrystalline model. It is shown that adiabatic variation in K introduces a time dependence into the angles which express the orientation of the molecular frame. The relevance of the adiabatic limit to the use of perturbed angular correlations of gamma radiation for study of the motion of radioactive species in viscous media is discussed.

Marshall, A. G.↗

Co-flow injection for serial crystallography at X-ray free-electron lasers

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

3D printing↗

Viscous Dissipation and Apparent Permeability of Gas Flow in Nanoporous Media

The nanopore confinement effect can increase the mobility for gas flow in shale rocks, and the apparent permeability is usually adopted to account for this effect. However, most of the apparent permeability calculation models are derived based on straight channels (capillaries) and neglect the influence of end effect. The end effect is caused by the bending of streamlines which yields more viscous dissipation and additional flow resistance for gas flow in nanoporous media. Here, for the first time the viscous dissipation for gas flow in nanoporous media is analyzed. In addition, an improved apparent permeability calculation model is proposed based on the Beskok-Karniadakis (B-K) model by introducing the influence of end effect, which is characterized by the ratio of the length to the width of a short channel (L/H). The accuracy of this model is validated by lattice Boltzmann simulations of gas flow in three different geometries: an infinite-length straight channel, a finite-length straight channel, and nanoporous media. For the infinite-length straight channel, there is no end effect therefore both the B-K model and the improved model can well predict the apparent permeability. However, for the finite-length straight channel and nanoporous media, the original B-K model overestimates the gas apparent permeability as it neglects the influence of end effect, while the improved model can still well predict the gas apparent permeability. In summary, the improved apparent permeability calculation model is more reasonable in predicting gas mobility in nanoporous media.

58 GEOSCIENCES↗

Porous Media and Mixture Models for Hygrothermal Behavior of Phenolic Composites

Theoretical models are proposed to describe the interaction of water with phenolic polymer. The theoretical models involve the study of the flow of a viscous fluid through a porous media and the thermodynamic theory of mixtures. From the theory, a set of mathematical relations are developed to simulate the effect of water on the thermostructural response of phenolic composites. The expressions are applied to simulate the measured effect of water in a series of experiments conducted on carbon phenolic composites.

Sullivan, Roy M.↗

A reciprocal theorem for a mixture of interacting continuous media

Using a linearized theory of interacting continuous media composed of linear elastic solid and linear viscous fluid, a reciprocal theorem is derived which relates the solution of one initial-boundary value problem to another. As an illustration of the reciprocal theorem, we obtain the early time displacement and velocity field of a mixture occupying an infinite region and subjected to an impulsively applied moving point load acting on the solid constituent.

Lee, Y. M.↗

Multiphase flow and granular mechanics

In this perspective we provide a brief overview of the state of knowledge and recent progress in the area of multiphase flow through deformable granular media. We show, with many examples, that the interplay between viscous, capillary, and frictional forces at the pore scale determines the mode of fluid invasion. We pay particular attention to the central role of wettability on the morphology of granular-pack deformation and failure. Beyond their intrinsic interest as processes that give rise to spectacular pattern formation, these coupled phenomena in granular media can control continental-scale fluxes like methane venting from the seafloor and geohazards like earthquakes and landslides. Finally, we conclude this perspective by pointing to fundamental knowledge gaps and exciting avenues of research.

42 ENGINEERING↗

Nonequilibrium Physics of Multiphase Flow in Porous Media: Wettability and Disorder

Carbon capture and geologic storage, dissociation of methane hydrates in permafrost, enhanced oil recovery, and water dropout in low-temperature fuel cells, all have something in common: two or more fluids flow simultaneously through a porous medium; and the displacement of one fluid by another is often unstable (either due to gravity or viscous forces). Yet, our ability to model multiphase flow in porous media has remained a challenge. The traditional equations are unable to predict, explain, or even reproduce, the formation of the complex patterns observed in experiments. The overarching goal of the project is to develop new physical understanding of the role of wettability and disorder in multiphase flow through permeable media, and to develop new mathematical and computational models at the pore scale and at the continuum scale.

58 GEOSCIENCES↗

Frontogenesis driven by horizontally quadratic distributions of density

Attention is given to the quadratic density distribution in a channel, which has been established by Simpson and Linden to be the simplest case of the horizontally nonlinear distribution of fluid density required for the production of frontogenesis. The porous-media and Boussinesq flow models are examined, and their evolution equations are reduced to one-dimensional systems. While both the porous-media and the inviscid/nondiffusive Boussinesq systems exhibit classic frontogenesis behavior, the viscous Boussinesq system exhibits a more complex behavior: boundary-layer effects force frontogenesis away from the lower boundary, and at late times the steepest density gradients are close to mid-channel.

Jacqmin, David↗

On some problems in a theory of thermally and mechanically interacting continuous media

Using a linearized theory of thermally and mechanically interacting mixture of linear elastic solid and viscous fluid, we derive a fundamental relation in an integral form called a reciprocity relation. This reciprocity relation relates the solution of one initial-boundary value problem with a given set of initial and boundary data to the solution of a second initial-boundary value problem corresponding to a different initial and boundary data for a given interacting mixture. From this general integral relation, reciprocity relations are derived for a heat-conducting linear elastic solid, and for a heat-conducting viscous fluid. An initial-boundary value problem is posed and solved for the mixture of linear elastic solid and viscous fluid. With the aid of the Laplace transform and the contour integration, a real integral representation for the displacement of the solid constituent is obtained as one of the principal results of the analysis.

Lee, Y. M.↗

Dynamics of Diffusion Flames in von Karman Swirling Flows Studied

Von Karman swirling flow is generated by the viscous pumping action of a solid disk spinning in a quiescent fluid media. When this spinning disk is ignited in an oxidizing environment, a flat diffusion flame is established adjacent to the disk, embedded in the boundary layer (see the preceding illustration). For this geometry, the conservation equations reduce to a system of ordinary differential equations, enabling researchers to carry out detailed theoretical models to study the effects of varying strain on the dynamics of diffusion flames. Experimentally, the spinning disk burner provides an ideal configuration to precisely control the strain rates over a wide range. Our original motivation at the NASA Glenn Research Center to study these flames arose from a need to understand the flammability characteristics of solid fuels in microgravity where slow, subbuoyant flows can exist, producing very small strain rates. In a recent work (ref. 1), we showed that the flammability boundaries are wider and the minimum oxygen index (below which flames cannot be sustained) is lower for the von Karman flow configuration in comparison to a stagnation-point flow. Adding a small forced convection to the swirling flow pushes the flame into regions of higher strain and, thereby, decreases the range of flammable strain rates. Experiments using downward facing, polymethylmethacrylate (PMMA) disks spinning in air revealed that, close to the extinction boundaries, the flat diffusion flame breaks up into rotating spiral flames (refs. 2 and 3). Remarkably, the dynamics of these spiral flame edges exhibit a number of similarities to spirals observed in biological systems, such as the electric pulses in cardiac muscles and the aggregation of slime-mold amoeba. The tail of the spiral rotates rigidly while the tip executes a compound, meandering motion sometimes observed in Belousov-Zhabotinskii reactions.

Nayagam, Vedha↗

Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of μNS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448–605 of μNS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP-μNS (448–605) crystallization in Sf9 cells was monitored and verified by several imaging techniques. Cells infected with the EGFP-μNS (448–605) baculovirus formed rod-shaped microcrystals (5–15 µm in length) which were reconstituted in high-viscosity media (LCP and agarose) and investigated by serial femtosecond X-ray diffraction using viscous jets at an X-ray free-electron laser (XFEL). The crystals diffracted to 4.5 Å resolution. A total of 4227 diffraction snapshots were successfully indexed into a hexagonal lattice with unit-cell parameters a = 109.29, b = 110.29, c = 324.97 Å. The final data set was merged and refined to 7.0 Å resolution. Preliminary electron-density maps were obtained. While more diffraction data are required to solve the structure of μNS (448–605) , the current experimental strategy, which couples high-viscosity crystal delivery at an XFEL with in cellulo crystallization, paves the way towards structure determination of the μNS protein.

59 BASIC BIOLOGICAL SCIENCES↗