Coulomb Final State Interactions for Gaussian Wave Packets

Two-particle like-sign and unlike-sign correlations including Coulomb final state interactions are calculated for Gaussian wave packets emitted from a Gaussian source. We show that the width of the wave packets can be fully absorbed into the spatial and momentum space widths of an effective emission function for plane wave states, and that Coulomb final state interaction effects are sensitive only to the latter, but not to the wave packet width itself. Results from analytical and numerical calculations are compared with recently published work by other authors.Comment: 10 pages Latex, 2 eps-figure

The role of the quantum dispersion in the Coulomb correction of Bose-Einstein correlations

The time dependent Schroedinger equation for two identical and charged pions is solved using wavepacket states. It is shown that the expected Coulomb distortion in the momentum correlation function is obliterated by the dispersion of the localized states, and therefore becomes unobservable.Comment: 10 pages, LaTeX, 2 figures, 0.2 Mb postscript, submitted to Phys. Lett.

Pseudochemotaxis in inhomogeneous active Brownian systems

We study dynamical properties of confined, self-propelled Brownian particles in an inhomogeneous activity profile. Using Brownian dynamics simulations, we calculate the probability to reach a fixed target and the mean first passage time to the target of an active particle. We show that both these quantities are strongly influenced by the inhomogeneous activity. When the activity is distributed such that high-activity zone is located between the target and the starting location, the target finding probability is increased and the passage time is decreased in comparison to a uniformly active system. Moreover, for a continuously distributed profile, the activity gradient results in a drift of active particle up the gradient bearing resemblance to chemotaxis. Integrating out the orientational degrees of freedom, we derive an approximate Fokker-Planck equation and show that the theoretical predictions are in very good agreement with the Brownian dynamics simulations.Comment: 7 pages, 5 figure

Numerical modelling of Bose-Einstein correlations

We propose extension of the algorithm for numerical modelling of Bose-Einstein correlations (BEC), which was presented some time ago in the literature. It is formulated on quantum statistical level for a single event and uses the fact that identical particles subjected to Bose statistics do bunch themselves, in a maximal possible way, in the same cells in phase-space. The bunching effect is in our case obtained in novel way allowing for broad applications and fast numerical calculations. First comparison with $e^+e^-$ annihilations data performed by using simple cascade hadronization model is very encouraging.Comment: LaTeX file and 5 eps file with figures, 9 pages altogethe

Facilitated diffusion of DNA-binding proteins

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.Comment: 4 pages, 2 figures Nov 22 2005 - accepted for PR

Modelling diffusional transport in the interphase cell nucleus

In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles, a random walk chain model, and a self avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the 3D geometry of the fiber network on the particle diffusion is investigated in detail, while varying occupation volume, chain length, persistence length and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self avoiding random walk model, and, to a lesser extent, the persistence length, affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve.Comment: 9 pages, 8 figure

Facilitated diffusion of DNA-binding proteins: Simulation of large systems

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be calibrated in numerical simulations inside a test system of moderate size. Once this is done, reaction times of systems of arbitrary dimensions are derived by extrapolation, with an accuracy of 10 to 15 percent. The achieved speed up, when compared to explicit simulations of the reaction process, is increasing proportional to the extrapolated volume of the cell.Comment: 8 pages, 4 figures, submitted to J. Chem. Phy