Limitation of finite element analysis of poroelastic behavior of biological tissues undergoing rapid loading

The finite element method is used in biomechanics to provide numerical solutions to simulations of structures having complex geometry and spatially differing material properties. Time-varying load deformation behaviors can result from solid viscoelasticity as well as viscous fluid flow through porous materials. Finite element poroelastic analysis of rapidly loaded slow-draining materials may be ill-conditioned, but this problem is not widely known in the biomechanics field. It appears as instabilities in the calculation of interstitial fluid pressures, especially near boundaries and between different materials. Accurate solutions can require impractical compromises between mesh size and time steps. This article investigates the constraints imposed by this problem on tissues representative of the intervertebral disc, subjected to moderate physiological rates of deformation. Two test cylindrical structures were found to require over 10(4) linear displacement-constant pressure elements to avoid serious oscillations in calculated fluid pressure. Fewer Taylor–Hood (quadratic displacement–linear pressure elements) were required, but with complementary increases in computational costs. The Vermeer–Verruijt criterion for 1D mesh size provided guidelines for 3D mesh sizes for given time steps. Pressure instabilities may impose limitations on the use of the finite element method for simulating fluid transport behaviors of biological soft tissues at moderately rapid physiological loading rates

A symmetry group of a Thue-Morse quasicrystal

We present a method of coding general self-similar structures. In particular, we construct a symmetry group of a one-dimensional Thue-Morse quasicrystal, i.e., of a nonperiodic ground state of a certain translation-invariant, exponentially decaying interaction.Comment: 6 pages, Late

Accurate structure factors from pseudopotential methods

Highly accurate experimental structure factors of silicon are available in the literature, and these provide the ideal test for any \emph{ab initio} method for the construction of the all-electron charge density. In a recent paper [J. R. Trail and D. M. Bird, Phys. Rev. B {\bf 60}, 7863 (1999)] a method has been developed for obtaining an accurate all-electron charge density from a first principles pseudopotential calculation by reconstructing the core region of an atom of choice. Here this method is applied to bulk silicon, and structure factors are derived and compared with experimental and Full-potential Linear Augmented Plane Wave results (FLAPW). We also compare with the result of assuming the core region is spherically symmetric, and with the result of constructing a charge density from the pseudo-valence density + frozen core electrons. Neither of these approximations provide accurate charge densities. The aspherical reconstruction is found to be as accurate as FLAPW results, and reproduces the residual error between the FLAPW and experimental results.Comment: 6 Pages, 3 figure

Geometry of jet spaces and integrable systems

An overview of some recent results on the geometry of partial differential equations in application to integrable systems is given. Lagrangian and Hamiltonian formalism both in the free case (on the space of infinite jets) and with constraints (on a PDE) are discussed. Analogs of tangent and cotangent bundles to a differential equation are introduced and the variational Schouten bracket is defined. General theoretical constructions are illustrated by a series of examples.Comment: 54 pages; v2-v6 : minor correction

Cooperative secretions facilitate host range expansion in bacteria

The majority of emergent human pathogens are zoonotic in origin, that is, they can transmit to humans from other animals. Understanding the factors underlying the evolution of pathogen host range is therefore of critical importance in protecting human health. There are two main evolutionary routes to generalism: organisms can tolerate multiple environments or they can modify their environments to forms to which they are adapted. Here we use a combination of theory and a phylogenetic comparative analysis of 191 pathogenic bacterial species to show that bacteria use cooperative secretions that modify their environment to extend their host range and infect multiple host species. Our results suggest that cooperative secretions are key determinants of host range in bacteria, and that monitoring for the acquisition of secreted proteins by horizontal gene transfer can help predict emerging zoonoses

Dissolution dominating calcification process in polar pteropods close to the point of aragonite undersaturation

Thecosome pteropods are abundant upper-ocean zooplankton that build aragonite shells. Ocean acidification results in the lowering of aragonite saturation levels in the surface layers, and several incubation studies have shown that rates of calcification in these organisms decrease as a result. This study provides a weight-specific net calcification rate function for thecosome pteropods that includes both rates of dissolution and calcification over a range of plausible future aragonite saturation states (Omega_Ar). We measured gross dissolution in the pteropod Limacina helicina antarctica in the Scotia Sea (Southern Ocean) by incubating living specimens across a range of aragonite saturation states for a maximum of 14 days. Specimens started dissolving almost immediately upon exposure to undersaturated conditions (Omega_Ar,0.8), losing 1.4% of shell mass per day. The observed rate of gross dissolution was different from that predicted by rate law kinetics of aragonite dissolution, in being higher at Var levels slightly above 1 and lower at Omega_Ar levels of between 1 and 0.8. This indicates that shell mass is affected by even transitional levels of saturation, but there is, nevertheless, some partial means of protection for shells when in undersaturated conditions. A function for gross dissolution against Var derived from the present observations was compared to a function for gross calcification derived by a different study, and showed that dissolution became the dominating process even at Omega_Ar levels close to 1, with net shell growth ceasing at an Omega_Ar of 1.03. Gross dissolution increasingly dominated net change in shell mass as saturation levels decreased below 1. As well as influencing their viability, such dissolution of pteropod shells in the surface layers will result in slower sinking velocities and decreased carbon and carbonate fluxes to the deep ocean

Sub-critical and Super-critical Regimes in Epidemic Models of Earthquake Aftershocks

We present an analytical solution and numerical tests of the epidemic-type aftershock (ETAS) model for aftershocks, which describes foreshocks, aftershocks and mainshocks on the same footing. The occurrence rate of aftershocks triggered by a single mainshock decreases with the time from the mainshock according to the modified Omori law K/(t+c)^p with p=1+theta. A mainshock at time t=0 triggers aftershocks according to the local Omori law, that in turn trigger their own aftershocks and so on. The effective branching parameter n, defined as the mean aftershock number triggered per event, controls the transition between a sub-critical regime n<1 to a super-critical regime n>1. In the sub-critical regime, we recover and document the crossover from an Omori exponent 1-theta for t<t* to 1+theta for t<t* found previously in [Sornette and Sornette, 1999a] for a special case of the ETAS model. In the super-critical regime n>1 and theta>0, we find a novel transition from an Omori decay law with exponent 1-theta fot t<t* to an explosive exponential increase of the seismicity rate fot t>t*. The case theta<0 yields an infinite n-value. In this case, we find another characteristic time tau controlling the crossover from an Omori law with exponent 1-theta for t<tau, similar to the local law, to an exponential increase at large times. These results can rationalize many of the stylized facts reported for aftershock and foreshock sequences, such as (i) the suggestion that a small p-value may be a precursor of a large earthquake, (ii) the relative seismic quiescence sometimes observed before large aftershocks, (iii) the positive correlation between b and p-values, (iv) the observation that great earthquakes are sometimes preceded by a decrease of b-value and (v) the acceleration of the seismicity preceding great earthquakes.Comment: Latex document of 41 pages + 6 eps figures + 1 tabl

Eigenvalue Problem in Two Dimension for An Irregular Boundary

An analytical perturbative method is suggested for solving the Helmholtz equation (\bigtriangledown^{2} + k^{2}){\psi} = 0 in two dimensions where {\psi} vanishes on an irregular closed curve. We can thus find the energy levels of a quantum mechanical particle confined in an infinitely deep potential well in two dimensions having an irregular boundary or the vibration frequencies of a membrane whose edge is an irregular closed curve. The method is tested by calculating the energy levels for an elliptical and a supercircular boundary and comparing with the results obtained numerically. Further, the phenomenon of level crossing due to shape variation is also discussed.Comment: 16 pages, 4 figures, v2 matches the journal versio