We computationally study the micromechanics of shear-induced size segregation and propose distinct migration mechanisms for individual large and small particles. While small particles percolate through voids without enduring contacts, large particles climb under shear through their crowded neighborhoods with anisotropic contact network. Particle rotation associated with shear is necessary for the upward migration of large particles. Segregation of large particles can be suppressed with inadequate friction, or with no rotation; increasing interparticle friction promotes the migration of large particles, but has little effect on the percolation of small particles.

SUMMARY Understanding the extent to which discrete element method (DEM) simulations can capture the critical state characteristics of granular materials is important to legitimize the use of DEM in geomechanics. This paper documents a DEM study that considered the sensitivity of the critical state response characteristics to the coefficient of interparticle friction (μ) using samples with gradings that are representative of a real soil. Most of the features that are typically associated with sand behaviour at the critical state were seen to emerge from the DEM simulation data. An important deviation occurs when high μ values (μ  ≥ 0.5) are used, as has been the case in a number of prior DEM studies. While there is a systematic variation in the critical state behaviour with μ for μ  < 0.5, when μ ≥ 0.5, the behaviour at the critical state seems to be insensitive to further increases in μ. In contrast to observations of conventional soil response, when μ ≥ 0.5, the void ratio at the critical state initially increases with increasing mean effective stress (p′). Analysis of the DEM data and use of simple models of isolated force chains enabled some key observations. When ‘floating’ particles that do not transmit stress are eliminated from the void ratio calculation, the void ratio at the critical state decreases consistently with increasing p′. There is a transition from sliding to rolling behaviour at the contact points as μ increases. Beyond a limiting value of μ, further increases in μ do not increase the buckling resistance of individual strong force chains. Copyright © 2014 John Wiley & Sons, Ltd.

SummaryComputational fluid dynamics and discrete element method (CFD–DEM) is extended with the volume of fluid (VOF) method to model free‐surface flows. The fluid is described on coarse CFD grids by solving locally averaged Navier–Stokes equations, and particles are modelled individually in DEM. Fluid–particle interactions are achieved by exchanging information between DEM and CFD. An advection equation is applied to solve the phase fraction of liquid, in the spirit of VOF, to capture the dynamics of free fluid surface. It also allows inter‐phase volume replacements between the fluid and solid particles. Further, as the size ratio (SR) of fluid cell to particle diameter is limited (i.e. no less than 4) in coarse‐grid CFD–DEM, a porous sphere method is adopted to permit a wider range of particle size without sacrificing the resolution of fluid grids. It makes use of more fluid cells to calculate local porosities. The developed solver (cfdemSolverVOF) is validated in different cases. A dam break case validates the CFD‐component and VOF‐component. Particle sedimentation tests validate the CFD–DEM interaction at various Reynolds numbers. Water‐level rising tests validate the volume exchange among phases. The porous sphere model is validated in both static and dynamic situations. Sensitivity analyses show that the SR can be reduced to 1 using the porous sphere approach, with the accuracy of analyses maintained. This allows more details of the fluid phase to be revealed in the analyses and enhances the applicability of the proposed model to geotechnical problems, where a highly dynamic fluid velocity and a wide range of particle sizes are encountered. Copyright © 2015 John Wiley & Sons, Ltd.

RNA G-quadruplex (rG4) structures are of fundamental importance to biology. A novel approach is introduced to detect and structurally map rG4s at single-nucleotide resolution in RNAs. The approach, denoted SHALiPE, couples selective 2'-hydroxyl acylation with lithium ion-based primer extension, and identifies characteristic structural fingerprints for rG4 mapping. We apply SHALiPE to interrogate the human precursor microRNA 149, and reveal the formation of an rG4 structure in this non-coding RNA. Additional analyses support the SHALiPE results and uncover that this rG4 has a parallel topology, is thermally stable, and is conserved in mammals. An in vitro Dicer assay shows that this rG4 inhibits Dicer processing, supporting the potential role of rG4 structures in microRNA maturation and post-transcriptional regulation of mRNAs.

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