Jure Dobnikar

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Lévy walks as a random search strategy have recently attracted a lot of attention, and have been described in many animal species. However, very little is known about one of the most important issues, namely how Lévy walks are generated by biological organisms. We study a model of the chemotaxis signaling pathway of E. coli, and demonstrate that stochastic(More)
Escherichia coli motion is characterized by a sequence of consecutive tumble-and-swim events. In the absence of chemical gradients, the length of individual swims is commonly believed to be distributed exponentially. However, recently there has been experimental indication that the swim-length distribution has the form of a power-law, suggesting that(More)
Molecular imprinting is the process whereby a polymer matrix is cross-linked in the presence of molecules with surface sites that can bind selectively to certain ligands on the polymer. The cross-linking process endows the polymer matrix with a chemical 'memory', such that the target molecules can subsequently be recognized by the matrix. We present a(More)
Double-stranded DNA (dsDNA) can trigger the production of type I interferon (IFN) in plasmacytoid dendritic cells (pDCs) by binding to endosomal Toll-like receptor-9 (TLR9; refs 1-5). It is also known that the formation of DNA-antimicrobial peptide complexes can lead to autoimmune diseases via amplification of pDC activation. Here, by combining X-ray(More)
Colloidal particles with DNA "legs" that can bind reversibly to receptors on a surface can be made to 'walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how controllable parameters, e.g. coating density and binding strength, affect the dynamics of such colloids. We find that(More)
We simulate the dynamics of a suspension of bacterial swimmers, which chemotactically sense gradients in either ambient or self-secreted attractants (e.g. nutrient or aspartate respectively), or in both. Unlike previous mean field models based on a set of continuum partial differential equations, our model resolves single swimmers and therefore incorporates(More)
We study the pattern formation in a two-dimensional system of superparamagnetic colloids interacting via spatially coherent induced interactions driven by an external precessing magnetic field. On the pair level, upon changing the opening angle of the external field, the interactions smoothly vary from purely repulsive (opening angle equal to zero) to(More)
Confinement can have a dramatic effect on the behavior of all sorts of particulate systems, and it therefore is an important phenomenon in many different areas of physics and technology. Here, we investigate the role played by the softness of the confining potential. Using grand canonical Monte Carlo simulations, we determine the phase diagram of(More)
In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the(More)