331 research outputs found
Dissimilar bouncy walkers
We consider the dynamics of a one-dimensional system consisting of dissimilar
hardcore interacting (bouncy) random walkers. The walkers' (diffusing
particles') friction constants xi_n, where n labels different bouncy walkers,
are drawn from a distribution rho(xi_n). We provide an approximate analytic
solution to this recent single-file problem by combining harmonization and
effective medium techniques. Two classes of systems are identified: when
rho(xi_n) is heavy-tailed, rho(xi_n)=A xi_n^(-1-\alpha) (0<alpha<1) for large
xi_n, we identify a new universality class in which density relaxations,
characterized by the dynamic structure factor S(Q,t), follows a Mittag-Leffler
relaxation, and the the mean square displacement of a tracer particle (MSD)
grows as t^delta with time t, where delta=alpha/(1+\alpha). If instead rho is
light-tailedsuch that the mean friction constant exist, S(Q,t) decays
exponentially and the MSD scales as t^(1/2). We also derive tracer particle
force response relations. All results are corroborated by simulations and
explained in a simplified model.Comment: 11 pages, to appear in Journal of Chemical Physic
Optimal target search on a fast folding polymer chain with volume exchange
We study the search process of a target on a rapidly folding polymer (`DNA')
by an ensemble of particles (`proteins'), whose search combines 1D diffusion
along the chain, Levy type diffusion mediated by chain looping, and volume
exchange. A rich behavior of the search process is obtained with respect to the
physical parameters, in particular, for the optimal search.Comment: 4 pages, 3 figures, REVTe
Fluctuation spectrum of quasispherical membranes with force-dipole activity
The fluctuation spectrum of a quasi-spherical vesicle with active membrane
proteins is calculated. The activity of the proteins is modeled as the proteins
pushing on their surroundings giving rise to non-local force distributions.
Both the contributions from the thermal fluctuations of the active protein
densities and the temporal noise in the individual active force distributions
of the proteins are taken into account. The noise in the individual force
distributions is found to become significant at short wavelengths.Comment: 9 pages, 2 figures, minor changes and addition
Ion pump activity generates fluctuating electrostatic forces in biomembranes
We study the non-equilibrium dynamics of lipid membranes with proteins that
actively pump ions across the membrane. We find that the activity leads to a
fluctuating force distribution due to electrostatic interactions arising from
variation in dielectric constant across the membrane. By applying a multipole
expansion we find effects on both the tension and bending rigidity dominated
parts of the membranes fluctuation spectrum. We discuss how our model compares
with previous studies of force-multipole models.Comment: 6 pages, 2 figures, to appear in EP
CRISPR/cas Loci of Type II Propionibacterium acnes Confer Immunity against Acquisition of Mobile Elements Present in Type I P. acnes
Propionibacterium acnes is a skin commensal that occasionally acts as an opportunistic pathogen. The population structure of this species shows three main lineages (I–III). While type I strains are mainly associated with sebaceous follicles of human skin and inflammatory acne, types II and III strains are more often associated with deep tissue infections. We investigated the occurrence and distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) in P. acnes, assessed their immunological memory, and addressed the question if such a system could account for type-specific properties of the species. A collection of 108 clinical isolates covering all known phylotypes of P. acnes was screened for the existence of CRISPR/cas loci. We found that CRISPR loci are restricted to type II P. acnes strains. Sequence analyses of the CRISPR spacers revealed that the system confers immunity to P. acnes-specific phages and to two mobile genetic elements. These elements are found almost exclusively in type I P. acnes strains. Genome sequencing of a type I P. acnes isolate revealed that one element, 54 kb in size, encodes a putative secretion/tight adherence (TAD) system. Thus, CRISPR/cas loci in P. acnes recorded the exposure of type II strains to mobile genetic elements of type I strains. The CRISPR/cas locus is deleted in type I strains, which conceivably accounts for their ability to horizontally acquire fitness or virulence traits and might indicate that type I strains constitute a younger subpopulation of P. acnes
Langevin formulation for single-file diffusion
We introduce a stochastic equation for the microscopic motion of a tagged
particle in the single file model. This equation provides a compact
representation of several of the system's properties such as
Fluctuation-Dissipation and Linear Response relations, achieved by means of a
diffusion noise approach. Most important, the proposed Langevin Equation
reproduces quantitatively the \emph{three} temporal regimes and the
corresponding time scales: ballistic, diffusive and subdiffusive.Comment: 9 pages, 5 figures, 1 table, to appear in Physical Review
Master equation approach to DNA-breathing in heteropolymer DNA
After crossing an initial barrier to break the first base-pair (bp) in
double-stranded DNA, the disruption of further bps is characterized by free
energies between less than one to a few kT. This causes the opening of
intermittent single-stranded bubbles. Their unzipping and zipping dynamics can
be monitored by single molecule fluorescence or NMR methods. We here establish
a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of
a master equation that governs the time evolution of the joint probability
distribution for the bubble size and position along the sequence. The transfer
coefficients are based on the Poland-Scheraga free energy model. We derive the
autocorrelation function for the bubble dynamics and the associated relaxation
time spectrum. In particular, we show how one can obtain the probability
densities of individual bubble lifetimes and of the waiting times between
successive bubble events from the master equation. A comparison to results of a
stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure
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