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.

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 ${R}^{- 3} $ or slower in interparticle distances) and that the diffusion matrix is positive definite, which is essential for Brownian dynamics modelling. Here, we extend the Rotne–Prager–Yamakawa approach to include both translational and rotational degrees of freedom, and derive the regularizing corrections to account for overlapping particles. Additionally, we show how the Rotne–Prager–Yamakawa approximation can be generalized for other geometries and boundary conditions.

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, nonlinear kinetics, and a finite-length system.

The Rotne–Prager–Yamakawa (RPY) approximation is a commonly used approach to model the hydrodynamic interactions between small spherical particles suspended in a viscous fluid at a low Reynolds number. However, when the particles overlap, the RPY tensors lose their positive definiteness, which leads to numerical problems in the Brownian dynamics simulations as well as errors in calculations of the hydrodynamic properties of rigid macromolecules using bead modelling. These problems can be avoided by using regularizing corrections to the RPY tensors; so far, however, these corrections have only been derived for equal-sized particles. Here we show how to generalize the RPY approach to the case of overlapping spherical particles of different radii and present the complete set of mobility matrices for such a system. In contrast to previous ad hoc approaches, our method relies on the direct integration of force densities over the sphere surfaces and thus automatically provides the correct limiting behaviour of the mobilities for the touching spheres and for a complete overlap, with one sphere immersed in the other one. This approach can then be used to calculate hydrodynamic properties of complex macromolecules using bead models with overlapping, different-sized beads, which we illustrate with an example.

We perform theoretical studies of stretching of 20 proteins with knots within a coarse-grained model. The knot’s 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.