Micromechanical study of elastic moduli of loose granular materials

In micromechanics of the elastic behaviour of granular materials, the macro-scale continuum elastic moduli are expressed in terms of micro-scale parameters, such as coordination number (the average number of contacts per particle) and interparticle contact stiffnesses in normal and tangential directions. It is well-known that mean-field theory gives inaccurate micromechanical predictions of the elastic moduli, especially for loose systems with low coordination number. Improved predictions of the moduli are obtained here for loose two-dimensional, isotropic assemblies. This is achieved by determining approximate displacement and rotation fields from the force and moment equilibrium conditions for small sub-assemblies of various sizes. It is assumed that the outer particles of these sub-assemblies move according to the mean field. From the particle displacement and rotation fields thus obtained, approximate elastic moduli are determined. The resulting predictions are compared with the true moduli, as determined from the discrete element method simulations for low coordination numbers and for various values of the tangential stiffness (at fixed value of the normal stiffness). Using this approach, accurate predictions of the moduli are obtained, especially when larger sub-assemblies are considered. As a step towards an analytical formulation of the present approach, it is investigated whether it is possible to replace the local contact stiffness matrices by a suitable average stiffness matrix. It is found that this generally leads to a deterioration of the accuracy of the predictions. Many micromechanical studies predict that the macroscopic bulk modulus is hardly influenced by the value of the tangential stiffness. It is shown here from the discrete element method simulations of hydrostatic compression that for loose systems, the bulk modulus strongly depends on the stiffness ratio for small stiffness ratios

Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors.

Protein kinase PKR (also known as EIF2AK2) is activated during viral infection and phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), leading to inhibition of translation and viral replication. We report fast evolution of the PKR kinase domain in vertebrates, coupled with positive selection of specific sites. Substitution of positively selected residues in human PKR with residues found in related species altered sensitivity to PKR inhibitors from different poxviruses. Species-specific differences in sensitivity to poxviral pseudosubstrate inhibitors were identified between human and mouse PKR, and these differences were traced to positively selected residues near the eIF2alpha binding site. Our findings indicate how an antiviral protein evolved to evade viral inhibition while maintaining its primary function. Moreover, the identified species-specific differences in the susceptibility to viral inhibitors have important implications for studying human infections in nonhuman model systems

Long Range Correlation in Granular Shear Flow II: Theoretical Implications

Numerical simulations are used to test the kinetic theory constitutive relations of inertial granular shear flow. These predictions are shown to be accurate in the dilute regime, where only binary collisions are relevant, but underestimate the measured value in the dense regime, where force networks of size $\xi$ are present. The discrepancy in the dense regime is due to non-collisional forces that we measure directly in our simulations and arise from elastic deformations of the force networks. We model the non-collisional stress by summing over all paths that elastic waves travel through force networks. This results in an analytical theory that successfully predicts the stress tensor over the entire inertial regime without any adjustable parameters

Interaction between the tRNA-Binding and C-Terminal Domains of Yeast Gcn2 Regulates Kinase Activity In Vivo

Citation: Lageix, S., Zhang, J. W., Rothenburg, S., & Hinnebusch, A. G. (2015). Interaction between the tRNA-Binding and C-Terminal Domains of Yeast Gcn2 Regulates Kinase Activity In Vivo. Plos Genetics, 11(2), 28. doi:10.1371/journal.pgen.1004991The stress-activated protein kinase Gcn2 regulates protein synthesis by phosphorylation of translation initiation factor eIF2 alpha. Gcn2 is activated in amino acid-deprived cells by binding of uncharged tRNA to the regulatory domain related to histidyl-tRNA synthetase, but the molecular mechanism of activation is unclear. We used a genetic approach to identify a key regulatory surface in Gcn2 that is proximal to the predicted active site of the HisRS domain and likely remodeled by tRNA binding. Mutations leading to amino acid substitutions on this surface were identified that activate Gcn2 at low levels of tRNA binding (Gcd(-) phenotype), while other substitutions block kinase activation (Gcn(-) phenotype), in some cases without altering tRNA binding by Gcn2 in vitro. Remarkably, the Gcn(-) substitutions increase affinity of the HisRS domain for the C-terminal domain (CTD), previously implicated as a kinase autoinhibitory segment, in a manner dampened by HisRS domain Gcd(-) substitutions and by amino acid starvation in vivo. Moreover, tRNA specifically antagonizes HisRS/CTD association in vitro. These findings support a model wherein HisRS-CTD interaction facilitates the autoinhibitory function of the CTD in nonstarvation conditions, with tRNA binding eliciting kinase activation by weakening HisRS-CTD association with attendant disruption of the autoinhibitory KD-CTD interaction

Unilateral interactions in granular packings: A model for the anisotropy modulus

Unilateral interparticle interactions have an effect on the elastic response of granular materials due to the opening and closing of contacts during quasi-static shear deformations. A simplified model is presented, for which constitutive relations can be derived. For biaxial deformations the elastic behavior in this model involves three independent elastic moduli: bulk, shear, and anisotropy modulus. The bulk and the shear modulus, when scaled by the contact density, are independent of the deformation. However, the magnitude of the anisotropy modulus is proportional to the ratio between shear and volumetric strain. Sufficiently far from the jamming transition, when corrections due to non-affine motion become weak, the theoretical predictions are qualitatively in agreement with simulation results.Comment: 6 pages, 5 figure

Periodic cells for large-scale problem initialization

In geotechnical applications the success of the discrete element method (DEM) in simulating fundamental aspects of soil behaviour has increased the interest in applications for direct simulation of engineering scale boundary value problems (BVP’s). The main problem is that the method remains relatively expensive in terms of computational cost. A non-negligible part of that cost is related to specimen creation and initialization. As the response of soil is strongly dependant on its initial state (stress and porosity), attaining a specified initial state is a crucial part of a DEM model. Different procedures for controlled sample generation are available. However, applying the existing REV-oriented initialization procedures to such models is inefficient in terms of computational cost and challenging in terms of sample homogeneity. In this work a simple but efficient procedure to initialize large-scale DEM models is presented. Periodic cells are first generated with a sufficient number of particles matching a desired particle size distribution (PSD). The cells are then equilibrated at low-level isotropic stress at target porosity. Once the cell is in equilibrium, it is replicated in space in order to fill the model domain. After the domain is thus filled a few mechanical cycles are needed to re-equilibrate the large domain. The result is a large, homogeneous sample, equilibrated under prescribed stress at the desired porosity. The method is applicable to both isotropic and anisotropic initial stress states, with stress magnitude varying in space

Solid behavior of anisotropic rigid frictionless bead assemblies

We investigate the structure and mechanical behavior of assemblies of frictionless, nearly rigid equal-sized beads, in the quasistatic limit, by numerical simulation. Three different loading paths are explored: triaxial compression, triaxial extension and simple shear. Generalizing recent results [1], we show that the material, despite rather strong finite sample size effects, is able to sustain a finite deviator stress in the macroscopic limit, along all three paths, without dilatancy. The shape of the yield surface is adequately described by a Lade-Duncan (rather than Mohr-Coulomb) criterion. While scalar state variables keep the same values as in isotropic systems, fabric and force anisotropies are each characterized by one parameter and are in one-to-one correspondence with principal stress ratio along all three loading paths.The anisotropy of the pair correlation function extends to a distance between bead surfaces on the order of 10% of the diameter. The tensor of elastic moduli is shown to possess a nearly singular, uniaxial structure related to stress anisotropy. Possible stress-strain relations in monotonic loading paths are also discussed

Force transmission in a packing of pentagonal particles

We perform a detailed analysis of the contact force network in a dense confined packing of pentagonal particles simulated by means of the contact dynamics method. The effect of particle shape is evidenced by comparing the data from pentagon packing and from a packing with identical characteristics except for the circular shape of the particles. A counterintuitive finding of this work is that, under steady shearing, the pentagon packing develops a lower structural anisotropy than the disk packing. We show that this weakness is compensated by a higher force anisotropy, leading to enhanced shear strength of the pentagon packing. We revisit "strong" and "weak" force networks in the pentagon packing, but our simulation data provide also evidence for a large class of "very weak" forces carried mainly by vertex-to-edge contacts. The strong force chains are mostly composed of edge-to-edge contacts with a marked zig-zag aspect and a decreasing exponential probability distribution as in a disk packing

Stress transmission in wet granular materials

We analyze stress transmission in wet granular media in the pendular state by means of three-dimensional molecular dynamics simulations. We show that the tensile action of capillary bonds induces a self-stressed particle network organized in two percolating "phases" of positive and negative particle pressures. Various statistical descriptors of the microstructure and bond force network are used to characterize this partition. Two basic properties emerge: 1) The highest particle pressure is located in the bulk of each phase; 2) The lowest pressure level occurs at the interface between the two phases, involving also the largest connectivity of the particles via tensile and compressive bonds. When a confining pressure is applied, the number of tensile bonds falls off and the negative phase breaks into aggregates and isolated sites

Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: Varying the number of double-stranded RNA binding domains and lineage-specific duplications

BackgroundDouble-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2alpha leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far.ResultsHere we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of PKR and PKZ in this latter species. Analyses of their genomic organization revealed up to three tandemly arrayed PKR genes, which are arranged in head-to-tail orientation. At least five duplications occurred independently in fish and amphibian lineages. Phylogenetic analyses reveal that the kinase domains of fish PKR genes are more closely related to those of fish PKZ than to the PKR kinase domains of other vertebrate species. The duplication leading to fish PKR and PKZ genes occurred early during teleost fish evolution after the divergence of the tetrapod lineage. While two dsRBDs are found in mammalian and amphibian PKR, one, two or three dsRBDs are present in fish PKR. In zebrafish, both PKR and PKZ were strongly upregulated after immunostimulation with some tissue-specific expression differences. Using genetic and biochemical assays we demonstrate that both zebrafish PKR and PKZ can phosphorylate eIF2alpha in yeast.ConclusionConsidering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both dsRNA and Z-DNA/RNA, and perhaps by altering sensitivity to viral PKR inhibitors. Further implications of our findings for the evolution of the PKR family and for studying PKR/PKZ interactions with viral gene products and their roles in viral infections are discussed