Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside of a narrow pore is obtained. With an analysis based on “electrohydrodynamic equivalence” we determine the possibility of e...

For the simulation of transport processes in porous media effective parameters for the physical processes on the target scale are equired. Numerical upscaling, as well as multiscale approaches can help where experiments are not possible, or hard to conduct. In 2009, Bastian and Engwer proposed an Unfitted Discontinuous Galerkin (UDG) method for solving PDEs in complex domains, .g. on the pore s...

In recent years, the Lattice Boltzmann (LB) method has become a powerful numerical tool for simulating complex fluid flows and modeling physics and chemistry in fluids. Derived from the continuum Boltzmann equation used in statistical mechanics, the LB method has the advantage of describing non-equilibrium dynamics, especially in fluid-flow applications involving interfacial dynamics and comple...

An accurate reservoir characterization is a crucial task for the development of quantitative geological models and reservoir simulation. In the present research work, a novel view is presented on the reservoir characterization using the advantages of thin section image analysis and intelligent classification algorithms. The proposed methodology comprises three main steps. First, four classes of...

A model was developed simulating reactive transport in groundwater including bioclogging. Results from a bioclogging experiment in a flow cell with a two-dimensional flow field were used as a data base to verify the simulation results of the model. Simulations were performed using three different hydraulic conductivity vs. porosity relations published in literature; two relations derived from p...

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 ...