Stochastic simulations of cargo transport by processive molecular motors

We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.Comment: 40 pages, Revtex with 13 figures, to appear in Journal of Chemical Physic

Consequences of self-consistency violations in Hartree-Fock random-phase approximation calculations of the nuclear breathing mode energy

We provide for the first time accurate assessments of the consequences of violations of self-consistency in the Hartree-Fock based random phase approximation (RPA) as commonly used to calculate the energy $E_c$ of the nuclear breathing mode. Using several Skyrme interactions we find that the self-consistency violated by ignoring the spin-orbit interaction in the RPA calculation causes a spurious enhancement of the breathing mode energy for spin unsaturated systems. Contrarily, neglecting the Coulomb interaction in the RPA or performing the RPA calculations in the TJ scheme underestimates the breathing mode energy. Surprisingly, our results for the $^{90}$Zr and $^{208}$Pb nuclei for several Skyrme type effective nucleon-nucleon interactions having a wide range of nuclear matter incompressibility ($K_{nm} \sim 215 - 275$ MeV) and symmetry energy ($J \sim 27 - 37$ MeV) indicate that the net uncertainty ($\delta E_c \sim 0.3$ MeV) is comparable to the experimental one.Comment: Revtex file (11 pages), Accepted for the publication in Phys. Rev.

Spatial separation of large dynamical blue shift and harmonic generation

We study the temporal and spatial dynamics of the large amplitude and frequency modulation that can be induced in an intense, few cycle laser pulse as it propagates through a rapidly ionizing gas. Our calculations include both single atom and macroscopic interactions between the non-linear medium and the laser field. We analyze the harmonic generation by such pulses and show that it is spatially separated from the ionization dynamics which produce a large dynamical blue shift of the laser pulse. This means that small changes in the initial laser focusing conditions can lead to large differences in the laser frequency modulation, even though the generated harmonic spectrum remains essentially unchanged.Comment: 4 pages, 5 figures. Under revisio