Five-Site Model for Brownian Dynamics Simulations of a Molecular Walker in Three Dimensions.

Motor proteins play an important role in many biological processes and have inspired the development of synthetic analogues. Molecular walkers, such as kinesin, dynein, and myosin V, fulfill a diverse set of functions including transporting cargo along tracks, pulling molecules through membranes, and deforming fibers. The complexity of molecular motors and their environment makes it difficult to model the detailed dynamics of molecular walkers over long time scales.

Organization of associating or crosslinked actin filaments in confinement.

A key factor of actin cytoskeleton organization in cells is the interplay between the dynamical properties of actin filaments and cell geometry, which restricts, confines and directs their orientation. Crosslinking interactions among actin filaments, together with geometrical cues and regulatory proteins can give rise to contractile rings in dividing cells and actin rings in neurons. Motivated by recent in vitro experiments, in this work we performed computer simulations to study basic aspects of the interplay between confinement and attractive interactions between actin filaments.

Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX.

Studies of how individual semi-flexible biopolymers and their network assemblies change over time reveal dynamical and mechanical properties important to the understanding of their function in tissues and living cells. Automatic tracking of biopolymer networks from fluorescence microscopy time-lapse sequences facilitates such quantitative studies. We present an open source software tool that combines a global and local correspondence algorithm to track biopolymer networks in 2D and 3D, using stretching open active contours.