First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metallorganic systems. Our results show that accurate Density-Functional Theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.Comment: 29 pages, 4 Postscript figures, revtex

Shell Model of Two-dimensional Turbulence in Polymer Solutions

We address the effect of polymer additives on two dimensional turbulence, an issue that was studied recently in experiments and direct numerical simulations. We show that the same simple shell model that reproduced drag reduction in three-dimensional turbulence reproduces all the reported effects in the two-dimensional case. The simplicity of the model offers a straightforward understanding of the all the major effects under consideration

Nonlinear envelope equation for broadband optical pulses in quadratic media

We derive a nonlinear envelope equation to describe the propagation of broadband optical pulses in second order nonlinear materials. The equation is first order in the propagation coordinate and is valid for arbitrarily wide pulse bandwidth. Our approach goes beyond the usual coupled wave description of $\chi^{(2)}$ phenomena and provides an accurate modelling of the evolution of ultra-broadband pulses also when the separation into different coupled frequency components is not possible or not profitable

Drag Reduction by Polymers in Turbulent Channel Flows: Energy Redistribution Between Invariant Empirical Modes

We address the phenomenon of drag reduction by dilute polymeric additive to turbulent flows, using Direct Numerical Simulations (DNS) of the FENE-P model of viscoelastic flows. It had been amply demonstrated that these model equations reproduce the phenomenon, but the results of DNS were not analyzed so far with the goal of interpreting the phenomenon. In order to construct a useful framework for the understanding of drag reduction we initiate in this paper an investigation of the most important modes that are sustained in the viscoelastic and Newtonian turbulent flows respectively. The modes are obtained empirically using the Karhunen-Loeve decomposition, allowing us to compare the most energetic modes in the viscoelastic and Newtonian flows. The main finding of the present study is that the spatial profile of the most energetic modes is hardly changed between the two flows. What changes is the energy associated with these modes, and their relative ordering in the decreasing order from the most energetic to the least. Modes that are highly excited in one flow can be strongly suppressed in the other, and vice versa. This dramatic energy redistribution is an important clue to the mechanism of drag reduction as is proposed in this paper. In particular there is an enhancement of the energy containing modes in the viscoelastic flow compared to the Newtonian one; drag reduction is seen in the energy containing modes rather than the dissipative modes as proposed in some previous theories.Comment: 11 pages, 13 figures, included, PRE, submitted, REVTeX

Transport–diffusion models with nonlinear boundary conditions and solution by generalized collocation methods

AbstractThis paper deals with the derivation of a class of nonlinear transport and diffusion models implemented with nonlinear boundary conditions. Mathematical tools to treat the initial-boundary value problems are developed, based on generalized collocation methods, focused on the treatment of nonlinear boundary conditions in one space dimension. Applications refer to a problem of interest in applied sciences