The initial stages of cave formation: Beyond the one-dimensional paradigm

The solutional origin of limestone caves was recognized over a century ago, but the short penetration length of an undersaturated solution made it seem impossible for long conduits to develop. This is contradicted by field observations, where extended conduits, sometimes several kilometers long, are found in karst environments. However, a sharp drop in the dissolution rate of CaCO_3 near saturation provides a mechanism for much deeper penetration of reactant. The notion of a "kinetic trigger" - a sudden change in rate constant over a narrow concentration range - has become a widely accepted paradigm in speleogenesis modeling. However, it is based on one-dimensional models for the fluid and solute transport inside the fracture, assuming that the dissolution front is planar in the direction perpendicular to the flow. Here we show that this assumption is incorrect; a planar dissolution front in an entirely uniform fracture is unstable to infinitesimal perturbations and inevitably breaks up into highly localized regions of dissolution. This provides an alternative mechanism for cave formation, even in the absence of a kinetic trigger. Our results suggest that there is an inherent wavelength to the erosion pattern in dissolving fractures, which depends on the reaction rate and flow rate, but is independent of the initial roughness. In contrast to one-dimensional models, two-dimensional simulations indicate that there is only a weak dependence of the breakthrough time on kinetic order; localization of the flow tends to keep the undersaturation in the dissolution front above the threshold for non-linear kinetics.Comment: to be published in Earth and Planetary Science Letter

Numerical Simulations of Particulate Suspensions via a Discretized Boltzmann Equation Part II. Numerical Results

A new and very general technique for simulating solid-fluid suspensions has been described in a previous paper (Part I); the most important feature of the new method is that the computational cost scales with the number of particles. In this paper (Part II), extensive numerical tests of the method are described; for creeping flows, both with and without Brownian motion, and at finite Reynolds numbers. Hydrodynamic interactions, transport coefficients, and the short-time dynamics of random dispersions of up to 1024 colloidal particles have been simulated.Comment: Text and figures in uuencode-tar-compressed postcript Email [email protected]

Reactive-infiltration instabilities in rocks. Fracture dissolution

A reactive fluid dissolving the surface of a uniform fracture will trigger an instability in the dissolution front, leading to spontaneous formation of pronounced well-spaced channels in the surrounding rock matrix. Although the underlying mechanism is similar to the wormhole instability in porous rocks there are significant differences in the physics, due to the absence of a steadily propagating reaction front. In previous work we have described the geophysical implications of this instability in regard to the formation of long conduits in soluble rocks. Here we describe a more general linear stability analysis, including axial diffusion, transport limited dissolution, non-linear kinetics, and a finite length system.Comment: to be published in J. Fluid. Mec

Statistical Mechanics of the Fluctuating Lattice Boltzmann Equation

We propose a new formulation of the fluctuating lattice Boltzmann equation that is consistent with both equilibrium statististical mechanics and fluctuating hydrodynamics. The formalism is based on a generalized lattice-gas model, with each velocity direction occupied by many particles. We show that the most probable state of this model corresponds to the usual equilibrium distribution of the lattice Boltzmann equation. Thermal fluctuations about this equilibrium are controlled by the mean number of particles at a lattice site. Stochastic collision rules are described by a Monte Carlo process satisfying detailed balance. This allows for a straightforward derivation of discrete Langevin equations for the fluctuating modes. It is shown that all non-conserved modes should be thermalized, as first pointed out by Adhikari et al.; any other choice violates the condition of detailed balance. A Chapman-Enskog analysis is used to derive the equations of fluctuating hydrodynamics on large length and time scales; the level of fluctuations is shown to be thermodynamically consistent with the equation of state of an isothermal, ideal gas. We believe this formalism will be useful in developing new algorithms for thermal and multiphase flows.Comment: Submitted to Physical Review E-11 pages Corrected Author(s) field on submittal for

Lattice Thermal Conductivity: A Comparison of Molecular Dynamics and Anharmonic Lattice Dynamics,” Phys.

The thermal conductivity of a monatomic face-centered-cubic lattice has been calculated over a range of temperatures from one-twentieth to one-half the melting temperature. An inverse-twelfth power "soft-sphere" potential was used to represent the interatomic forces. We have examined, quantitatively, the approximations involved in deriving the Peierls phonon-transport expression for the thermal conductivity and have determined the temperature range over which it is useful. This has involved extensive comparisons with the formally exact Green-Kubo method, using molecular dynamics to generate the phase-space trajectories. At low temperatures, the relaxation processes in a crystal can be described in terms of phonon lifetimes. We have calculated the lifetimes of all the phonon states of 108-, 256-, and 864-particle classical crystals, with periodic boundaries, by molecu lar dynamics and by anharmonic perturbation theory. These lifetimes were then used to estimate the thermal conductivity.~

A symplectic integration method for elastic filaments

A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then difficult to ensure that the Hamiltonian structure of the exact equations is preserved. Here we discretize the Hamiltonian itself, expressed as a line integral over the contour of the filament. This discrete representation of the continuum filament can then be integrated by one of the explicit symplectic integrators frequently used in molecular dynamics. The model systematically approximates the continuum partial differential equations, but has the same level of computational complexity as molecular dynamics and is constraint free. Numerical tests show that the algorithm is much more stable than a finite-difference formulation and can be used for high aspect ratio filaments, such as actin

Fluctuating Motor Forces Bend Growing Microtubules

Despite their rigidity, microtubules in living cells bend significantly during polymerization resulting in greater curvature than can be explained by thermal forces alone. However, the source of the non-thermal forces that bend growing microtubules remains obscure. We analyzed the motion of microtubule tips in NIH-3T3 fibroblasts expressing EGFP-EB1, a fluorescent +TIP protein that specifically binds to the growing ends of microtubules. We found that dynein inhibition significantly reduced the deviation of the growing tip from its initial trajectory. Inhibiting myosin modestly reduced tip fluctuations, while simultaneous myosin and dynein inhibition caused no further decrease in fluctuations compared to dynein inhibition alone. Our results can be interpreted with a model in which dynein linkages play a key role in generating and transmitting fluctuating forces that bend growing microtubules.National Institutes of Health (U.S.) (NIH GM102486)National Science Foundation (U.S.) (NSF CMMI 0954302, NSF CMMI 0927945, and NSF CTS-0505929

A comparison of the static and dynamic properties of a semi-flexible polymer using lattice-Boltzmann and Brownian dynamics simulations

The aim of this paper is to compare results from lattice-Boltzmann and Brownian dynamics simulations of linear chain molecules. We have systematically varied the parameters that may affect the accuracy of the lattice-Boltzmann simulations, including grid resolution, temperature, polymer mass, and fluid viscosity. The effects of the periodic boundary conditions are minimized by an analytic correction for the different long-range interactions in periodic and unbounded systems. Lattice-Boltzmann results for the diffusion coefficient and Rouse mode relaxation times were found to be insensitive to temperature, which suggests that effects of hydrodynamic retardation are small. By increasing the resolution of the lattice-Boltzmann grid with respect to the polymer size, convergent results for the diffusion coefficient and relaxation times were obtained; these results agree with Brownian dynamics to within 1--2%.Comment: Corrected LB reduced time step ($\Delta t/t_0$) in Fig. 1 and Table