Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum

We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature‐dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.     

A Reidemeister trace for fibred maps

A Reidemeister trace for fibred maps is defined as the alternating sum of suitable (elementary) traces for linear morphisms of fibred cellular free modules with local coefficients. This invariant extends in a natural way the classical construction of the generalized Lefschetz number??Reidemeister trace??to the category of fibred CW-complexes.     

Impact of PDL-induced crosstalk on 100-Gb/s polarization-multiplexed RZ-DQPSK in PMD-affected metro networks

The impact of PDL-induced crosstalk on 100-Gb/s polarization-multiplexed RZ-DQPSK performance in direct detection systems is experimentally assessed in presence of a moderate amount of PMD. In particular, RZ-interleaving and RZ-overlapping schemes have shown opposite behaviours towards PMD and PDL. Measurements carried out confirm the less robustness of RZ-interleaving than RZ-overlapping towards PMD, but highlight a much stronger tolerance of RZ-interleaving to PDL with respect to RZ-overlapping. When PDL combines with moderate PMD, as in metro networks, it is shown that RZ-overlapping high tolerance to PMD drastically fails, RZ-interleaving proving more efficient to deal with polarization issues in case of direct detection of polarization-multiplexed signals.     

Self-amplified spontaneous emission free-electron laser with an energy-chirped electron beam and undulator tapering

We report the first experimental implementation of a method based on simultaneous use of an energy chirp in the electron beam and a tapered undulator, for the generation of ultrashort pulses in a self-amplified spontaneous emission mode free-electron laser (SASE FEL). The experiment, performed at the SPARC FEL test facility, demonstrates the possibility of compensating the nominally detrimental effect of the chirp by a proper taper of the undulator gaps. An increase of more than 1 order of magnitude in the pulse energy is observed in comparison to the untapered case, accompanied by FEL spectra where the typical SASE spiking is suppressed.     

A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA‐Intercalator Salphen‐Type ZnII Complex

The photophysical and DNA‐binding properties of the cationic zinc(II) complex of 5‐triethylammonium methyl salicylidene ortho‐phenylenediiminato (ZnL²⁺) were investigated by a combination of experimental and theoretical methods. DFT calculations were performed on both the ground and the first excited states of ZnL²⁺ and on its possible mono‐ and dioxidation products, both in vacuo and in selected solvents mimicked by the polarizable continuum model. Comparison of the calculated absorption and fluorescence transitions with the corresponding experimental data led to the conclusion that visible light induces a two‐electron photooxidation process located on the phenylenediiminato ligand. Kinetic measurements, performed by monitoring absorbance changes over time in several solvents, are in agreement with a slow unimolecular photooxidation process, which is faster in water and slower in less polar solvents. Moreover, structural details of ZnL–DNA binding were obtained by DFT calculations on the intercalation complexes between ZnL and the d(ApT)₂ and d(GpC)₂ dinucleoside monophosphate duplexes. Two main complementary binding interactions are proposed: 1) intercalation of the central phenyl ring of the ligand between the stacked DNA base pairs; 2) external electrostatic attraction between the negatively charged phosphate groups and the two cationic triethylammonium groups of the Schiff‐base ligand. Such suggestions are supported by fluorescence titrations performed on the ZnL/DNA system at different ionic strengths and temperatures. In particular, the values of the DNA‐binding constants obtained at different temperatures provided the enthalpic and entropic contributions to the binding and confirmed that two competitive mechanisms, namely, intercalation and external interaction, are involved. The two mechanisms are coexistent at room temperature under physiological conditions.     

On the local convergence of an iterative approach for inverse singular value problems

The purpose of this paper is to provide the convergence theory for the iterative approach given by M.T. Chu [Numerical methods for inverse singular value problems, SIAM J. Numer. Anal. 29 (1992), pp. 885–903] in the context of solving inverse singular value problems. We provide a detailed convergence analysis and show that the ultimate rate of convergence is quadratic in the root sense. Numerical results which confirm our theory are presented. It is still an open issue to prove that the method is Q-quadratic convergent as claimed by M.T. Chu.     

Planar central configurations as fixed points

Planar central configurations can be seen as critical points of the reduced potential or solutions of a system of equations. By the homogeneity of the potential and its O(2)-invariance it is possible to see that the SO(2)- orbits of central configurations are fixed points of a map f. The purpose of the paper is to define and study this map and to derive some properties using topological fixed point theory. The generalized Moulton–Smale theorem for collinear configurations is proved, together with some estimates on the number of central configurations in the case of three bodies, using fixed point indices. Well-known results such as the compactness of the set of central configurations follow easily in this topological framework. Dedicated to Professor Albrecht Dold and Professor Edward Fadell     

Itinerant oscillation with a cosine potential

The equations of motion of the planar itinerant librator are extended to involve a cosine potential rather than a harmonic form for interaction, and are solved numerically to produce the angular velocity autocorrelation function and its Fourier transform (real and imaginary parts). The behaviour of the cosine potential is matched with that of the harmonic potential through these functions and in general conforms more closely to the indication of zero-THz spectroscopy and computer simulation.