Reply to Comment on "Critical analysis of a variational method used to describe molecular electron transport"

We show that the failure of the Delaney-Greer (DG) variational ansatz for transport demonstrated by us in Phys.\ Rev.\ B {\bf 80}, 165301 (2009) (I) is not related to an unsuitable constraint that prevents a broken time-reversal symmetry or to real orbitals, as DG incorrectly claim. The complex orbitals suggested by them as a way-out solution merely represent a particular case of the general case considered by us in I, which do not in the least affect our conclusion.Comment: Manuscript as submitted to Phys. Rev. B on 30 November 2010. Sections VII, VIII, and IX present significant details, which enlarge the analysis of the published versio

DIAGNOSTIC ANALYSIS OF THE COST PER UNIT OF PRODUCT

This paper treats the methodology used in the product unit diagnostic analysis by entities where products are obtained in several subordinated entities with management autonomy. It also presents the relations based on which overall effects of the structural changes on cost per product unit are quantified, as well as the relations used in the analysis of some calculation items.cost per product unit; structure; constant costs; variable costs

Rotating magnetic field actuation of a multicilia configuration

This paper was presented at the 2nd Micro and Nano Flows Conference (MNF2009), which was held at Brunel University, West London, UK. The conference was organised by Brunel University and supported by the Institution of Mechanical Engineers, IPEM, the Italian Union of Thermofluid dynamics, the Process Intensification Network, HEXAG - the Heat Exchange Action Group and the Institute of Mathematics and its Applications.The current paper continues the analysis of a completely novel method of fluid manipulation technology in micro-fluidics systems, inspired by nature, namely by the mechanisms found in ciliates. More information on this subject can be found at http://www.hitech-projects.com/euprojects/artic/. In order to simulate the drag forces acting on an array of artificial cilia, we have developed a computer code that is based on fundamental solutions of Stokes flow in a semi-infinite domain. The actuation mechanism consists of a bi-directional rotating excitation magnetic field. The magnetization induced by the magnetic field was calculated in a separate routine based on the Integral Nonlinear Equations Approach with 1D discretization of wire (cilium). Time averaged x-coordinate mass flow rates are computed for several cilium configurations resulting. The outcome and originality of this paper consist on assessing magnetic actuation as a practical tool for obtaining a consistent one-directional fluid flow.This work has been supported through grant ARTIC FP6-2004-NMP-TI4

Ferromagnetic resonance study of Co/Pd/Co/Ni multilayers with perpendicular anisotropy irradiated with Helium ions

We present a ferromagnetic resonance (FMR) study of the effect of Helium ion irradiation on the magnetic anisotropy, the linewidth and the Gilbert damping of a Co/Ni multilayer coupled to Co/Pd bilayers. The perpendicular magnetic anisotropy decreases linearly with He ion fluence, leading to a transition to in-plane magnetization at a critical fluence of 5x10^{14} ions/cm^2. We find that the damping is nearly independent of fluence but the FMR linewidth at fixed frequency has a maximum near the critical fluence, indicating that the inhomogeneous broadening of the FMR line is a non-monotonic function of the He ion fluence. Based on an analysis of the angular dependence of the FMR linewidth, the inhomogeneous broadening is associated with spatial variations in the magnitude of the perpendicular magnetic anisotropy. These results demonstrate that ion irradiation may be used to systematically modify the magnetic anisotropy and distribution of magnetic anisotropy parameters of Co/Pd/Co/Ni multilayers for applications and basic physics studies

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let

Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 BChls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy

On a method to calculate conductance by means of the Wigner function: two critical tests

We have implemented the linear response approximation of a method proposed to compute the electron transport through correlated molecules based on the time-independent Wigner function [P. Delaney and J. C. Greer, \prl {\bf 93}, 36805 (2004)]. The results thus obtained for the zero-bias conductance through quantum dot both without and with correlations demonstrate that this method is either quantitatively nor qualitatively able to provide a correct physical escription of the electric transport through nanosystems. We present an analysis indicating that the failure is due to the manner of imposing the boundary conditions, and that it cannot be simply remedied.Comment: 22 pages, 7 figur

Global Schr\"{o}dinger maps

We consider the Schr\"{o}dinger map initial-value problem in dimension two or greater. We prove that the Schr\"{o}dinger map initial-value problem admits a unique global smooth solution, provided that the initial data is smooth and small in the critical Sobolev space. We prove also that the solution operator extends continuously to the critical Sobolev space.Comment: 60 page

Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality

In general, the direct application of the Jarzynski equality (JE) to reconstruct potentials of mean force (PMFs) from a small number of nonequilibrium unidirectional steered molecular dynamics (SMD) paths is hindered by the lack of sampling of extremely rare paths with negative dissipative work. Such trajectories, that transiently violate the second law, are crucial for the validity of JE. As a solution to this daunting problem, we propose a simple and efficient method, referred to as the FR method, for calculating simultaneously both the PMF U(z) and the corresponding diffusion coefficient D(z) along a reaction coordinate z for a classical many particle system by employing a small number of fast SMD pullings in both forward (F) and time reverse (R) directions, without invoking JE. By employing Crook's transient fluctuation theorem (that is more general than JE) and the stiff spring approximation, we show that: (i) the mean dissipative work W_d in the F and R pullings are equal, (ii) both U(z) and W_d can be expressed in terms of the easily calculable mean work of the F and R processes, and (iii) D(z) can be expressed in terms of the slope of W_d. To test its viability, the FR method is applied to determine U(z) and D(z) of single-file water molecules in single-walled carbon nanotubes (SWNTs). The obtained U(z) is found to be in very good agreement with the results from other PMF calculation methods, e.g., umbrella sampling. Finally, U(z) and D(z) are used as input in a stochastic model, based on the Fokker-Planck equation, for describing water transport through SWNTs on a mesoscopic time scale that in general is inaccessible to MD simulations.Comment: ReVTeX4, 13 pages, 6 EPS figures, Submitted to Journal of Chemical Physic