Piotr Szymczak

Wormhole formation in dissolving fractures

[1] We investigate the dissolution of artificial fractures with three-dimensional, pore-scale numerical simulations. The fluid velocity in the fracture space was determined from a lattice Boltzmann method, and a stochastic solver was used for the transport of dissolved species. Numerical simulations were used to study conditions under which long conduits (wormholes) form in an initially rough but spatially homogeneous fracture. The effects of flow rate, mineral dissolution rate, and geometrical properties of the fracture were investigated, and the optimal conditions for wormhole formation were determined.

Stabilizing effect of knots on proteins

Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.

Tightening of knots in proteins.

We perform theoretical studies of stretching of 20 proteins with knots within a coarse-grained model. The knots ends are found to jump to well defined sequential locations that are associated with sharp turns, whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Knots typically do not return to their native locations when a protein is released after stretching.

Drag force on a sphere moving towards a corrugated wall

From the solution of the creeping-flow equations, the drag force on a sphere becomes infinite when the gap between the sphere and a smooth wall vanishes at constant velocity, so that if the sphere is displaced towards the wall with a constant applied force, contact theoretically may not occur. Physically, the drag is finite for various reasons, one being the particle and wall roughness. Then, for vanishing gap, even though some layers of fluid molecules may be left between the particle and wall roughness peaks, conventionally it may be said that contact occurs. In this paper, we consider the example of a smooth sphere moving towards a rough wall. The roughness considered here consists of parallel periodic wedges, the wavelength of which is small compared with the sphere radius. This problem is considered both experimentally and theoretically. The motion of a millimetre size bead settling towards a corrugated horizontal wall in a viscous oil is measured with laser interferometry giving an accuracy on the displacement of 0.1

Proteins in a shear flow.

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Hydrodynamic effects in proteins

m. Several wedge-shaped walls were used, with various wavelengths and wedge angles. From the results, it is observed that the velocity of the sphere is, except for small gaps, similar to that towards a smooth plane that is shifted down from the top of corrugations. Indeed, earlier theories for a shear flow along a corrugated wall found such an equivalent smooth plane. These theories are revisited here. The creeping flow is calculated as a series in the slope of the roughness grooves. The cases of a flow along and across the grooves are considered separately. The shift is larger in the former case. Slightly flattened tops of the wedges used in experiments are also considered in the calculations. It is then demonstrated that the effective shift for the sphere motion is the average of the shifts for shear flows in the two perpendicular directions. A good agreement is found between theory and experiment.

Generalization of the Rotne-Prager-Yamakawa mobility and shear disturbance tensors

The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and find that at moderate shear rates they unfold through a sequence of metastable states-a pattern which is distinct from a smooth unraveling found in homopolymers. Full unfolding occurs only at very large shear rates. Furthermore, the hydrodynamic interactions between the amino acids are shown to hinder the shear flow unfolding. The characteristics of the unfolding process depend on whether a protein is anchored or not, and if it is, on the choice of an anchoring point.

Stretching of proteins in a uniform flow

Experimental and numerical results pertaining to flow-induced effects in proteins are reviewed. Special emphasis is placed on shear-induced unfolding and on the role of solvent mediated hydrodynamic interactions in the conformational transitions in proteins.

Reactive-infiltration instabilities in rocks. Fracture dissolution

The Rotne–Prager–Yamakawa approximation is one of the most commonly used methods of including hydrodynamic interactions in modelling of colloidal suspensions and polymer solutions. The two main merits of this approximation are that it includes all long-range terms (i.e. decaying as

Three-particle contribution to sedimentation and collective diffusion in hard-sphere suspensions

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