Benchmarking calculations of excitonic couplings between bacteriochlorophylls

Excitonic couplings between (bacterio)chlorophyll molecules are necessary for simulating energy transport in photosynthetic complexes. Many techniques for calculating the couplings are in use, from the simple (but inaccurate) point-dipole approximation to fully quantum-chemical methods. We compared several approximations to determine their range of applicability, noting that the propagation of experimental uncertainties poses a fundamental limit on the achievable accuracy. In particular, the uncertainty in crystallographic coordinates yields an uncertainty of about 20% in the calculated couplings. Because quantum-chemical corrections are smaller than 20% in most biologically relevant cases, their considerable computational cost is rarely justified. We therefore recommend the electrostatic TrEsp method across the entire range of molecular separations and orientations because its cost is minimal and it generally agrees with quantum-chemical calculations to better than the geometric uncertainty. We also caution against computationally optimizing a crystal structure before calculating couplings, as it can lead to large, uncontrollable errors. Understanding the unavoidable uncertainties can guard against striving for unrealistic precision; at the same time, detailed benchmarks can allow important qualitative questions--which do not depend on the precise values of the simulation parameters--to be addressed with greater confidence about the conclusions

Level-rank duality via tensor categories

We give a new way to derive branching rules for the conformal embedding (\asl_n)_m\oplus(\asl_m)_n\subset(\asl_{nm})_1. In addition, we show that the category \Cc(\asl_n)_m^0 of degree zero integrable highest weight (\asl_n)_m-representations is braided equivalent to \Cc(\asl_m)_n^0 with the reversed braiding.Comment: 16 pages, to appear in Communications in Mathematical Physics. Version 2 changes: Proof of main theorem made explicit, example 4.11 removed, references update

Bivariate spline interpolation with optimal approximation order

Let be a triangulation of some polygonal domain f c R2 and let S9 (A) denote the space of all bivariate polynomial splines of smoothness r and degree q with respect to A. We develop the first Hermite-type interpolation scheme for S9 (A), q >_ 3r + 2, whose approximation error is bounded above by Kh4+i, where h is the maximal diameter of the triangles in A, and the constant K only depends on the smallest angle of the triangulation and is independent of near-degenerate edges and nearsingular vertices. Moreover, the fundamental functions of our scheme are minimally supported and form a locally linearly independent basis for a superspline subspace of Sr, (A). This shows that the optimal approximation order can be achieved by using minimally supported splines. Our method of proof is completely different from the quasi-interpolation techniques for the study of the approximation power of bivariate splines developed in [71 and [181

Cylindrically symmetric solitons in Einstein-Yang-Mills theory

Recently new Einstein-Yang-Mills (EYM) soliton solutions were presented which describe superconducting strings with Kasner asymptotic (hep-th/0610183). Here we study the static cylindrically symmetric SU(2) EYM system in more detail. The ansatz for the gauge field corresponds to superposition of the azimuthal $B_\phi$ and the longitudinal $B_z$ components of the color magnetic field. We derive sum rules relating data on the symmetry axis to asymptotic data and show that generic asymptotic structure of regular solutions is Kasner. Solutions starting with vacuum data on the axis generically are divergent. Regular solutions correspond to some bifurcation manifold in the space of parameters which has the low-energy limiting point corresponding to string solutions in flat space (with the divergent total energy) and the high-curvature point where gravity is crucial. Some analytical results are presented for the low energy limit, and numerical bifurcation curves are constructed in the gravitating case. Depending on the parameters, the solution looks like a straight string or a pair of straight and circular strings. The existence of such non-linear superposition of two strings becomes possible due to self-interaction terms in the Yang-Mills action which suppress contribution of the circular string near the polar axis.Comment: 21 pages, 11 figure

Solitons on H-bonds in proteins

A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs in three dimensions the formalism of fully integrable Toda lattices which admits phonons as well as solitons along the hydrogen-bonds of the helices. A simulation of the three dimensional Toda lattice system shows that the solitons are spontaneously created and are stable and moving along the helix axis. A perturbation on one of the three H-bond lines forms solitons on the other H-bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm$^{-1}$ which are found in recent X-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins.Comment: 6 pages, 7 figure

Coherent charge transport through molecular wires: "Exciton blocking" and current from electronic excitations in the wire

We consider exciton effects on current in molecular nanojunctions, using a model comprising a two two-level sites bridge connecting free electron reservoirs. Expanding the density operator in the many-electron eigenstates of the uncoupled sites, we obtain a 16X16 density matrix in the bridge subspace whose dynamics is governed by Liuoville equation that takes into account interactions on the bridge as well as electron injection and damping to and from the leads. Our consideration can be considerably simplified by using the pseudospin description based on the symmetry properties of Lie group SU(2). We study the influence of the bias voltage, the Coulomb repulsion and the energy-transfer interactions on the steady-state current and in particular focus on the effect of the excitonic interaction between bridge sites. Our calculations show that in case of non-interacting electrons this interaction leads to reduction in the current at high voltage for a homodimer bridge. In other words, we predict the effect of \textquotedblleft exciton\textquotedblright blocking. The effect of \textquotedblleft exciton\textquotedblright blocking is modified for a heterodimer bridge, and disappears for strong Coulomb repulsion at sites. In the latter case the exciton type interactions can open new channels for electronic conduction. In particular, in the case of strong Coulomb repulsion, conduction exists even when the electronic connectivity does not exist.Comment: 14 pages, 15 figure

Synthesis and spectral properties of colloidal solutions of metal sulfides

Cadmium, lead, and zinc sulfides as well as cadmium and lead (cadmium and zinc) complex sulfides have been synthesized in the colloidal state by reaction of metal trifluoroacetates with thioacetamide in ethyl acetate and methylmethacrylate. Synthesis products have been isolated from the reaction solutions and studied by X-ray diffraction, vibrational and electronic spectroscopy, and electronic microscopy. The effect of the composition on spectral properties of formulations has been discussed. The formation of colloidal particles and the stability of solutions are related to the complexation