Time-dependent DFT studies of metal core-electron excitations in Mn complexes

Time-dependent density functional theory (TDDFT) has been applied to study core excitations from 1s and 2p Mn orbitals in a series of manganese complexes with oxygen and nitrogen donor ligands. The effect of basis set and functional on the excitation energy was evaluated in detail for one complex, Mn(acac)2 x (H2O)2. The results obtained for a range of compounds, namely, [Mn(Im)6]Cl2, Mn(CH3COO)2 x 4 H2O, Mn(acac)3, Mn(SALADHP)2 and [Mn(SALPN)O]2, show good consistency with the data from X-ray absorption spectroscopy (XAS), confirming the relation between the Mn K-edge energy and the oxidation state of the Mn atom. The energies predicted for 2p core excitations show a dependence on the metal oxidation state very similar to that determined experimentally by 1s2p resonant inelastic X-ray scattering (RIXS) studies for Mn(acac)2 x (H2O)2, Mn(acac)3, and Mn(sal)2(bipy). The reliability of the K-edge energies obtained in the present study indicates that TDDFT can be used in determining the oxidation states of Mn atoms in different computational models of the manganese cluster of photosystem II (PSII).     

The completion of locally refined simplicial partitions created by bisection

Recently, in [Found. Comput. Math., 7(2) (2007), 245-269], we proved that an adaptive finite element method based on newest vertex bisection in two space dimensions for solving elliptic equations, which is essentially the method from [SINUM, 38 (2000), 466-488] by Morin, Nochetto, and Siebert, converges with the optimal rate.The number of triangles in the output partition of such a method is generally larger than the number of triangles that in all intermediate partitions have been marked for bisection, because additional bisections are needed to retain conforming meshes.A key ingredient to our proof was a result from [Numer. Math., 97(2004), 219-268] by Binev, Dahmen and DeVore saying that for some absolute constant , where is the number of triangles from the initial partition that have never been bisected. In this paper, we extend this result to bisection algorithms of -simplices, with that generalizing the result concerning optimality of the adaptive finite element method to general space dimensions.

     

Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds

We conduct computational analyses of ion permeation characteristics in a model glycine receptor (GlyR) modified by photo-sensitive compounds. In particular, we consider hypothetical attachment to the channel of charge-neutral chemical groups which can be photo-activated by shining light of an appropriate wavelength on the system. After illumination, the attached molecules become charged via a photodissociation process or excited into a charge-separated state (thus generating a significant electric dipole). We carry out Brownian Dynamics simulations of ion flow through the channel in the presence of the additional charges generated in this fashion. Based on these calculations, we predict that photo-activation of appropriately positioned photo-sensitive compounds near the channel mouth can significantly modify the rate of ion permeation and the current rectification ratio. Possible implications for GlyR-based device designs are briefly discussed.     

Adaptive frame methods for elliptic operator equations: the steepest descent approach

Massimo Fornasier^¶ Dipartimento di Metodi e Modelli Matematici per le Scienze Applicate, Università "La Sapienza" in Roma, Via Antonio Scarpa, 16/B, I-00161 Roma, Italy Rob Stevenson^|| Department of Mathematics, Utrecht University, PO Box 80.010, NL-3508 TA Utrecht, The Netherlands ^{This paper is concerned with the development of adaptive numericalmethods for elliptic operator equations. We are particularlyinterested in discretization schemes based on wavelet frames.We show that by using three basic subroutines an implementable,convergent scheme can be derived, which, moreover, has optimalcomputational complexity. The scheme is based on adaptive steepestdescent iterations. We illustrate our findings by numericalresults for the computation of solutions of the Poisson equationwith limited Sobolev smoothness on intervals in 1D and L-shapeddomains in 2D.}     

Strong inhibition of cholera toxin binding by galactose dendrimers

Galactose-containing dendrimers with long spacer arms inhibit cholera toxin binding as strongly as the natural ganglioside GM1 oligosaccharide does.     

Measuring flux distributions for diffusion in the small-numbers limit

For the classical diffusion of independent particles, Fick's law gives a well-known relationship between the average flux and the average concentration gradient. What has not yet been explored experimentally, however, is the dynamical distribution of diffusion rates in the limit of small particle numbers. Here, we measure the distribution of diffusional fluxes using a microfluidics device filled with a colloidal suspension of a small number of microspheres. Our experiments show that (1) the flux distribution is accurately described by a Gaussian function; (2) Fick's law, that the average flux is proportional to the particle gradient, holds even for particle gradients down to a single particle difference; (3) the variance in the flux is proportional to the sum of the particle numbers; and (4) there are backward flows, where particles flow up a concentration gradient, rather than down it. In addition, in recent years, two key theorems about nonequilibrium systems have been introduced: Evans' fluctuation theorem for the distribution of entropies and Jarzynski's work theorem. Here, we introduce a new fluctuation theorem, for the fluxes, and we find that it is confirmed quantitatively by our experiments.