Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics.

Microscopic semiflexible filaments suspended in a viscous fluid are widely encountered in biophysical problems. The classic example is the flagella used by microorganisms to generate propulsion. Simulating the dynamics of these filaments numerically is complicated because of the coupling between the motion of the filament and that of the surrounding fluid. An attractive idea is to simplify this coupling by modeling the fluid motion by using Stokeslets distributed at equal intervals along the model filament. We show that, with an appropriate choice of the hydrodynamic radii, one can recover accurate hydrodynamic behavior of a filament with a finite cross section without requiring an explicit surface. This is true, however, only if the hydrodynamic radii take specific values and that they differ in the parallel and perpendicular directions leading to a caterpillarlike hydrodynamic shape. Having demonstrated this, we use the model to compare with analytic theory of filament deformation and rotation in the small deformation limit. Generalization of the methodology, including application to simulations using the Rotne-Prager tensor, is discussed.

Single-molecule observation of anomalous electrohydrodynamic orientation of microtubules.

We use fluorescence microscopy to measure the orientation and shape of microtubules-which serve as a model system for semiflexible rods-that are electrophoretically driven. Surprisingly, a bimodal orientation distribution is observed, with microtubules in either parallel or perpendicular orientations to the electric field. The occupancy of these states varies nonmonotonically with the microtubule length L and the electric field E. We also observe a surprising bending deformation of microtubules. Interestingly, all data collapse onto a universal scaling curve when the average alignment is plotted as a function of B proportional, variantEL3, which reflects the ratio between the driving force and a restoring elastic force. Our results have important implications for the interpretation of electrical birefringence experiments and, more generally, for a better understanding of the electrokinetics of rods.

DIA-MCIS: an importance sampling network randomizer for network motif discovery and other topological observables in transcription networks.

MOTIVATION: Transcription networks, and other directed networks can be characterized by some topological observables (e.g. network motifs), that require a suitable randomized network ensemble, typically with the same degree sequences of the original ones. The commonly used algorithms sometimes have long convergence times, and sampling problems. We present here an alternative, based on a variant of the importance sampling Monte Carlo developed by (Chen et al.). AVAILABILITY: The algorithm is available at http://wwwteor.mi.infn.it/bassetti/downloads.html

Random networks tossing biased coins.

In statistical mechanical investigations of complex networks, it is useful to employ random graph ensembles as null models to compare with experimental realizations. Motivated by transcription networks, we present here a simple way to generate an ensemble of random directed graphs with asymptotically, scale-free out-degree and compact in-degree. Entries in each row of the adjacency matrix are set to 0 or 1 according to the toss of a biased coin, with a chosen probability distribution for the biases. This defines a quick and simple algorithm, which yields good results already for graphs of size n approximately 100. Perhaps more importantly, many of the relevant observables are accessible analytically, improving upon previous estimates for similar graphs. The technique is easily generalizable to different kinds of graphs.

Sedimentation of pairs of hydrodynamically interacting semiflexible filaments.

We describe the effect of hydrodynamic interactions in the sedimentation of a pair of inextensible semiflexible filaments under a uniform constant force at low Reynolds numbers. We have analyzed the different regimes and the morphology of such polymers in simple geometries, which allow us to highlight the peculiarities of the interplay between elastic and hydrodynamic stresses. Cooperative and symmetry breaking effects associated to the geometry of the fibers gives rise to characteristic motion which give them distinct properties from rigid and elastic filaments.