Conformal Mapping on Rough Boundaries II: Applications to bi-harmonic problems

We use a conformal mapping method introduced in a companion paper to study the properties of bi-harmonic fields in the vicinity of rough boundaries. We focus our analysis on two different situations where such bi-harmonic problems are encountered: a Stokes flow near a rough wall and the stress distribution on the rough interface of a material in uni-axial tension. We perform a complete numerical solution of these two-dimensional problems for any univalued rough surfaces. We present results for sinusoidal and self-affine surface whose slope can locally reach 2.5. Beyond the numerical solution we present perturbative solutions of these problems. We show in particular that at first order in roughness amplitude, the surface stress of a material in uni-axial tension can be directly obtained from the Hilbert transform of the local slope. In case of self-affine surfaces, we show that the stress distribution presents, for large stresses, a power law tail whose exponent continuously depends on the roughness amplitude

Permeability of self-affine rough fractures

The permeability of two-dimensional fractures with self-affine fractal roughness is studied via analytic arguments and numerical simulations. The limit where the roughness amplitude is small compared with average fracture aperture is analyzed by a perturbation method, while in the opposite case of narrow aperture, we use heuristic arguments based on lubrication theory. Numerical simulations, using the lattice Boltzmann method, are used to examine the complete range of aperture sizes, and confirm the analytic arguments.Comment: 11 pages, 9 figure

Roughness of fracture surfaces

We study the fracture surface of three dimensional samples through a model for quasi-static fractures known as Born Model. We find for the roughness exponent a value of 0.5 expected for ``small length scales'' in microfracturing experiments. Our simulations confirm that at small length scales the fracture can be considered as quasi-static. The isotropy of the roughness exponent on the crack surface is also shown. Finally, considering the crack front, we compute the roughness exponents for longitudinal and transverse fluctuations of the crack line (both 0.5). They result in agreement with experimental data, and supports the possible application of the model of line depinning in the case of long-range interactions.Comment: 10 pages, 5 figures, Late

Internal states of model isotropic granular packings. III. Elastic properties

In this third and final paper of a series, elastic properties of numerically simulated isotropic packings of spherical beads assembled by different procedures and subjected to a varying confining pressure P are investigated. In addition P, which determines the stiffness of contacts by Hertz's law, elastic moduli are chiefly sensitive to the coordination number, the possible values of which are not necessarily correlated with the density. Comparisons of numerical and experimental results for glass beads in the 10kPa-10MPa range reveal similar differences between dry samples compacted by vibrations and lubricated packings. The greater stiffness of the latter, in spite of their lower density, can hence be attributed to a larger coordination number. Voigt and Reuss bounds bracket bulk modulus B accurately, but simple estimation schemes fail for shear modulus G, especially in poorly coordinated configurations under low P. Tenuous, fragile networks respond differently to changes in load direction, as compared to load intensity. The shear modulus, in poorly coordinated packings, tends to vary proportionally to the degree of force indeterminacy per unit volume. The elastic range extends to small strain intervals, in agreement with experimental observations. The origins of nonelastic response are discussed. We conclude that elastic moduli provide access to mechanically important information about coordination numbers, which escape direct measurement techniques, and indicate further perspectives.Comment: Published in Physical Review E 25 page

Intermittency of velocity time increments in turbulence

We analyze the statistics of turbulent velocity fluctuations in the time domain. Three cases are computed numerically and compared: (i) the time traces of Lagrangian fluid particles in a (3D) turbulent flow (referred to as the "dynamic" case); (ii) the time evolution of tracers advected by a frozen turbulent field (the "static" case), and (iii) the evolution in time of the velocity recorded at a fixed location in an evolving Eulerian velocity field, as it would be measured by a local probe (referred to as the "virtual probe" case). We observe that the static case and the virtual probe cases share many properties with Eulerian velocity statistics. The dynamic (Lagrangian) case is clearly different; it bears the signature of the global dynamics of the flow.Comment: 5 pages, 3 figures, to appear in PR

Frictionless bead packs have macroscopic friction, but no dilatancy

The statement of the title is shown by numerical simulation of homogeneously sheared packings of frictionless, nearly rigid beads in the quasistatic limit. Results coincide for steady flows at constant shear rate γ in the limit of small γ and static approaches, in which packings are equilibrated under growing deviator stresses. The internal friction angle ϕ, equal to 5.76 $\pm$ 0.22 degrees in simple shear, is independent on the average pressure P in the rigid limit. It is shown to stem from the ability of stable frictionless contact networks to form stress-induced anisotropic fabrics. No enduring strain localization is observed. Dissipation at the macroscopic level results from repeated network rearrangements, like the effective friction of a frictionless slider on a bumpy surface. Solid fraction Φ remains equal to the random close packing value ≃ 0.64 in slowly or statically sheared systems. Fluctuations of stresses and volume are observed to regress in the large system limit, and we conclude that the same friction law for simple shear applies in the large psystem limit if normal stress or density is externally controlled. Defining the inertia number as I = γ m/(aP), with m the grain mass and a its diameter, both internal friction coefficient $\mu$∗ = tan ϕ and volume 1/Φ increase as powers of I in the quasistatic limit of vanishing I, in which all mechanical properties are determined by contact network geometry. The microstructure of the sheared material is characterized with a suitable parametrization of the fabric tensor and measurements of connectivity and coordination numbers associated with contacts and near neighbors.Comment: 19 pages. Additional technical details may be found in v

An algorithm to calculate the transport exponent in strip geometries

An algorithm for solving the random resistor problem by means of the transfer-matrix approach is presented. Preconditioning by spanning clusters extraction both reduces the size of the conductivity matrix and speed up the calculations.Comment: 17 pages, RevTeX2.1, HLRZ - 97/9

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

From Individual to Collective Pinning: Effect of Long-range Elastic Interactions

We study the effect of long-range elastic interactions in the dynamical behavior of an elastic chain driven quasi-statically in a quenched random pinning potential and in the strong pinning limit. This is a generic situation occuring in solid friction, crack propagation, wetting front motion, ... Tuning the exponent of the algebraic decay of the elastic interaction with the distance is shown to give rise to three regimes: a Mean-Field (MF) regime, a Laplacian (L) regime and an intermediate regime where the critical exponents interpolate continuously between the MF and L limit cases. The effect of the driving mode on the avalanche statistics is also analyzed.Comment: 28 pages in RevTex, 17 figure

Electrostatic free energy calculations using the generalized solvent boundary potential method

Copyright 2002 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.1507108.Free energyperturbation (FEP) calculations using all-atom molecular dynamics simulations with a large number of explicit solvent molecules are a powerful approach to study ligand–macromolecule association processes at the atomic level. One strategy to carry out FEP calculations efficiently and reduce computational time is to consider the explicit dynamics of only a small number of atoms in a localized region around the ligand. Such an approximation is motivated by the observation that the factors governing binding specificity are dominated by interactions in the vicinity of the ligand. However, a straightforward truncation of the system may yield inaccurate results as the influence exerted by the remote regions of the macromolecule and the surrounding solvent through long-range electrostatic effects may be significant. To obtain meaningful results, it is important to incorporate the influence of the remote regions of the ligand–macromolecule complex implicitly using some effective potential. The generalized solvent boundary potential (GSBP) that was developed recently [W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)] is an efficient computational method to represent the long-range electrostaticinteractions arising from remote (outer) regions in simulations of a localized (inner) region with a small number of explicit atoms. In the present work, FEP calculations combined with GSBP are used to illustrate the importance of these long-range electrostatic factors in estimation of the charging free energy of an aspartate ligand bound to the aspartyl-tRNA synthetase. Calculations with explicit spherical simulation inner regions of different radii are used to test the accuracy of the GSBP method and also illustrate the importance of explicit protein and solvent dynamics in the free energy estimation. The influence of the represented outer region is tested using separate simulations in which the reaction field and/or the protein static field are excluded. Both components are shown to be essential to obtain quantitatively meaningful results. The ability of implicitly treating the influence of protein fluctuations in the outer region using a protein dielectric constant is examined. It is shown that accurate charging free energy calculations can be performed for this system with a spherical region of 15 to 20 Å radius, which roughly corresponds to 1500–3500 moving atoms. The results indicate that GSBP in combination with FEP calculations is a precise and efficient approach to include long-range electrostatic effects in the study of ligand binding to large macromolecules