How and why does willow biochar increase a clay soil water retention capacity?

Addition of biochar into a soil changes its water retention properties by modifying soil textural and structural properties. In addition, internal micrometer-scale porosity that is able to directly store readily plant available water affects soil water retention properties. This study shows how precise knowledge of the internal micrometer-scale pore size distribution of biochar can deepen the understanding of the biochar-water interactions in soils. The micrometer-scale porosity of willow biochar was quantitatively and qualitatively characterized using X-ray tomography, 3D image analysis and Helium ion microscopy. The effect of biochar application on clay soil water retention was studied by…

Protein diffusion in mammalian cell cytoplasm.

We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribut…

Visualization in the integrated SimPhoNy multiscale simulation framework

Abstract We describe three distinct approaches to visualization for multiscale materials modelling research. These have been developed with the framework of the SimPhoNy FP7 EU-project, and complement each other in their requirements and possibilities. All have been integrated via wrappers to one or more of the simulation approaches within the SimPhoNy project. In this manuscript we describe and contrast their features. Together they cover visualization needs from electronic to macroscopic scales and are suited to simulations made on personal computers, workstations or advanced High Performance parallel computers. Examples as well as recommendations for future calculations are presented.

Effects of pyrolysis temperature on the hydrologically relevant porosity of willow biochar

Biochar pore space consists of porosity of multiple length scales. In direct water holding applications like water storage for plant water uptake, the main interest is in micrometre-range porosity since these pores are able to store water that is easily available for plants. Gas adsorption measurements which are commonly used to characterize the physical pore structure of biochars are not able to quantify this pore-size range. While pyrogenetic porosity (i.e. pores formed during pyrolysis process) tends to increase with elevated process temperature, it is uncertain whether this change affects the pore space capable to store plant available water. In this study, we characterized biochar poro…

A boundary condition for arbitrary shaped inlets in lattice-Boltzmann simulations

We introduce a mass-flux-based inlet boundary condition for the lattice-Boltzmann method. The proposed boundary condition requires minimal amount of boundary data, it produces a steady-state velocity field which is accurate close to the inlet even for arbitrary inlet geometries, and yet it is simple to implement. We demonstrate its capability for both simple and complex inlet geometries by numerical experiments. For simple inlet geometries, we show that the boundary condition provides very accurate inlet velocities when Re less than or similar to 1. Even with moderate Reynolds number, the inlet velocities are accurate for practical purposes. Furthermore, the potential of our boundary condit…

Comparison of implementations of the lattice-Boltzmann method

AbstractSimplicity of coding is usually an appealing feature of the lattice-Boltzmann method (LBM). Conventional implementations of LBM are often based on the two-lattice or the two-step algorithm, which however suffer from high memory consumption and poor computational performance, respectively. The aim of this work was to identify implementations of LBM that would achieve high computational performance with low memory consumption. Effects of memory addressing schemes were investigated in particular. Data layouts for velocity distribution values were also considered, and they were found to be related to computational performance. A novel bundle data layout was therefore introduced. Address…

Simulation Software for Flow of Fluid with Suspended Point Particles in Complex Domains: Application to Matrix Diffusion

Matrix diffusion is a phenomenon in which tracer particles convected along a flow channel can diffuse into porous walls of the channel, and it causes a delay and broadening of the breakthrough curve of a tracer pulse. Analytical and numerical methods exist for modeling matrix diffusion, but there are still some features of this phenomenon, which are difficult to address using traditional approaches. To this end we propose to use the lattice-Boltzmann method with point-like tracer particles. These particles move in a continuous space, are advected by the flow, and there is a stochastic force causing them to diffuse. This approach can be extended to include particle-particle and particle-wall…

A prospect for computing in porous materials research: Very large fluid flow simulations

Abstract Properties of porous materials, abundant both in nature and industry, have broad influences on societies via, e.g. oil recovery, erosion, and propagation of pollutants. The internal structure of many porous materials involves multiple scales which hinders research on the relation between structure and transport properties: typically laboratory experiments cannot distinguish contributions from individual scales while computer simulations cannot capture multiple scales due to limited capabilities. Thus the question arises how large domain sizes can in fact be simulated with modern computers. This question is here addressed using a realistic test case; it is demonstrated that current …

Application of the lattice-Boltzmann method to multiphase flows

Mass-flux-based outlet boundary conditions for the lattice Boltzmann method

We present outlet boundary conditions for the lattice Boltzmann method. These boundary conditions are constructed with a mass-flux-based approach. Conceptually, the mass-flux-based approach provides a mathematical framework from which specific boundary conditions can be derived by enforcing given physical conditions. The object here is, in particular, to explain the mass-flux-based approach. Furthermore, we illustrate, transparently, how boundary conditions can be derived from the emerging mathematical framework. For this purpose, we derive and present explicitly three outlet boundary conditions. By construction, these boundary conditions have an apparent physical interpretation which is fu…

Impalement transitions in droplets impacting microstructured superhydrophobic surfaces

Liquid droplets impacting a superhydrophobic surface decorated with micro-scale posts often bounce off the surface. However, by decreasing the impact velocity droplets may land on the surface in a fakir state, and by increasing it posts may impale droplets that are then stuck on the surface. We use a two-phase lattice-Boltzmann model to simulate droplet impact on superhydrophobic surfaces, and show that it may result in a fakir state also for reasonable high impact velocities. This happens more easily if the surface is made more hydrophobic or the post height is increased, thereby making the impaled state energetically less favourable.

Strain hardening in liquid-particle suspensions

The behavior of a liquid-particle suspension induced to sheared motion was analyzed by numerical simulations. When the velocity (strain) of the suspension began to increase, its viscosity first stayed almost constant, but increased then rapidly to a clearly higher level. This increase in viscosity is shown to be related to formation of clusters of suspended particles. Clusters are shown to increase the viscosity by enhanced momentum transfer though clustered particles. This is the mechanism behind the strain-hardening phenomenon observed in small-strain experiments on liquid-particle suspensions.

Using microtomography, image analysis and flow simulations to characterize soil surface seals

Raindrops that impact on soil surface affect the pore structure and form compact soil surface seals. Damaged pore structure reduces water infiltration which can lead to increased soil erosion. We introduce here methods to characterize the properties of surface seals in a detailed manner. These methods include rainfall simulations, x-ray microtomography, image analysis and pore-scale flow simulations. Methods were tested using clay soil samples, and the results indicate that the sealing process changes several properties of the pore structure.

Publisher’s Note: Strain hardening in liquid-particle suspensions [Phys. Rev. E72, 061402 (2005)]

Coupling of lattice-Boltzmann solvers with suspended particles using the MPI intercommunication framework

Abstract The MPI intercommunication framework was used for coupling of two lattice-Boltzmann solvers with suspended particles, which model advection and diffusion respectively of these particles in a carrier fluid. Simulation domain was divided into two parts, one with advection and diffusion, and the other with diffusion only (no macroscopic flow). Particles were exchanged between these domains at their common boundary by a direct process to process communication. By analysing weak and strong scaling, it was shown that the linear scaling characteristics of the lattice-Boltzmann solvers were not compromised by their coupling.

Slip Flow Over Structured Surfaces with Entrapped Microbubbles

On hydrophobic surfaces, roughness may lead to a transition to a superhydrophobic state, where gas bubbles at the surface can have a strong impact on a detected slip. We present two-phase lattice Boltzmann simulations of a Couette flow over structured surfaces with attached gas bubbles. Even though the bubbles add slippery surfaces to the channel, they can cause negative slip to appear due to the increased roughness. The simulation method used allows the bubbles to deform due to viscous stresses. We find a decrease of the detected slip with increasing shear rate which is in contrast to some recent experimental results implicating that bubble deformation cannot account for these experiments.…

Dependence of thermal conductivity on structural parameters in porous samples

The in-plane thermal conductivity of porous sintered bronze plates was studied both experimentally and numerically. We developed and validated an experimental setup, where the sample was placed in vacuum and heated while its time-dependent temperature field was measured with an infrared camera. The porosity and detailed three-dimensional structure of the samples were determined by X-ray microtomography. Lattice-Boltzmann simulations of thermal conductivity in the tomographic reconstructions of the samples were used to correct the contact area between bronze particles as determined by image analysis from the tomographic reconstructions. Small openings in the apparent contacts could not be de…

Simulation of liquid penetration in paper

Capillary penetration of a wetting liquid in a microtomographic image of paper board, whose linear dimension was close to the average length of wood fibers, was simulated by the lattice-Boltzmann method. In spite of the size of the system not being large with respect to the size of structural inhomogeneities in the sample, for unidirectional penetration the simulated behavior was described well by that of the Lucas-Washburn equation, while for radial penetration a radial capillary equation described the behavior. In both cases the average penetration depth of the liquid front as a function of time followed a power law over many orders of magnitude. Capillary penetration of small droplets of…

Intrusion of nonwetting liquid in paper

The saturation curve of a sample of paper board was measured with mercury-intrusion porosimetry, and the three-dimensional structure of its pore space was determined by x-ray tomographic imaging. Ab initio numerical simulation of intrusion on the tomographic reconstruction, based on the lattice-Boltzmann method, was in excellent agreement with the measured saturation curve. A numerical invasion-percolation simulation in the same tomographic reconstruction showed good agreement with the lattice-Boltzmann simulation. The access function of the sample, determined from the saturation curve and the pore-throat distribution determined from the tomographic reconstruction, indicated that the ink-bo…

Lattice Boltzmann simulations in microfluidics: probing the no-slip boundary condition in hydrophobic, rough, and surface nanobubble laden microchannels

In this contribution we review recent efforts on investigations of the effect of (apparent) boundary slip by utilizing lattice Boltzmann simulations. We demonstrate the applicability of the method to treat fundamental questions in microfluidics by investigating fluid flow in hydrophobic and rough microchannels as well as over surfaces covered by nano- or microscale gas bubbles.

Evaluation of a lattice-Boltzmann method for mercury intrusion porosimetry simulations

We have simulated intrusion of a non-wetting liquid into pores of varying shape and size. Simulations were based on the lattice-Boltzmann method and the Shan–Chen multiphase model. The liquid–solid contact angle for pores with circular cross-section was found to be equal to that for pores with square cross-section, and constant even for small pore sizes if the discretised shape of the circular cross-section was taken into account. For comparison, contact angle was also determined for a liquid column descending in a capillary tube, and the results were found to be consistent. Application of the method to mercury intrusion porosimetry is discussed.

An efficient swap algorithm for the lattice Boltzmann method

During the last decade, the lattice-Boltzmann method (LBM) as a valuable tool in computational fluid dynamics has been increasingly acknowledged. The widespread application of LBM is partly due to the simplicity of its coding. The most well-known algorithms for the implementation of the standard lattice-Boltzmann equation (LBE) are the two-lattice and two-step algorithms. However, implementations of the two-lattice or the two-step algorithm suffer from high memory consumption or poor computational performance, respectively. Ultimately, the computing resources available decide which of the two disadvantages is more critical. Here we introduce a new algorithm, called the swap algorithm, for t…