1,362 research outputs found
Collective dynamics effect transient subdiffusion of inert tracers in gel networks
Based on extensive Brownian dynamics simulations we study the thermally
driven motion of a tracer bead in a cross-linked, dynamic gel network in the
limit when the tracer bead's size is of the same size or even larger than the
equilibrium mesh size of the gel. The analysis of long individual trajectories
of the tracer bead demonstrates the existence of pronounced transient anomalous
diffusion, accompanied by a drastic slow-down of the gel-bead relaxation
dynamics. From the time averaged mean squared displacement and the van Hove
cross-correlation function we elucidate the many-body origin of the
non-Brownian tracer bead dynamics. Our results shed new light on the ongoing
debate over the physical origin of sterical tracer interactions with structured
environments.Comment: 5 pages, 4 figures, RevTe
Real sequence effects on the search dynamics of transcription factors on DNA
Recent experiments show that transcription factors (TFs) indeed use the
facilitated diffusion mechanism to locate their target sequences on DNA in
living bacteria cells: TFs alternate between sliding motion along DNA and
relocation events through the cytoplasm. From simulations and theoretical
analysis we study the TF-sliding motion for a large section of the DNA-sequence
of a common E. coli strain, based on the two-state TF-model with a fast-sliding
search state and a recognition state enabling target detection. For the
probability to detect the target before dissociating from DNA the TF-search
times self-consistently depend heavily on whether or not an auxiliary operator
(an accessible sequence similar to the main operator) is present in the genome
section. Importantly, within our model the extent to which the interconversion
rates between search and recognition states depend on the underlying nucleotide
sequence is varied. A moderate dependence maximises the capability to
distinguish between the main operator and similar sequences. Moreover, these
auxiliary operators serve as starting points for DNA looping with the main
operator, yielding a spectrum of target detection times spanning several orders
of magnitude. Auxiliary operators are shown to act as funnels facilitating
target detection by TFs.Comment: 26 pages, 7 figure
Efficient Computation of Image Persistence
We present an algorithm for computing the barcode of the image of a morphism in persistent homology induced by an inclusion of filtered finite-dimensional chain complexes. The algorithm makes use of the clearing optimization and can be applied to inclusion-induced maps in persistent absolute homology and persistent relative cohomology for filtrations of pairs of simplicial complexes. The clearing optimization works particularly well in the context of relative cohomology, and using previous duality results we can translate the barcodes of images in relative cohomology to those in absolute homology. This forms the basis for an implementation of image persistence computations for inclusions of filtrations of Vietoris-Rips complexes in the framework of the software Ripser
- …