A variational approach for calculating Franck-Condon factors including mode-mode anharmonic coupling

We have implemented our new procedure for computing Franck-Condon factors utilizing vibrational configuration interaction based on a vibrational self-consistent field reference. Both Duschinsky rotations and anharmonic three-mode coupling are taken into account. Simulations of the first ionization band of Cl O2 and C4 H4 O (furan) using up to quadruple excitations in treating anharmonicity are reported and analyzed. A developer version of the MIDASCPP code was employed to obtain the required anharmonic vibrational integrals and transition frequencies

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Conformations of poly{G}-poly{C} π stacks with high hole mobility

Charge transfer properties of DNA depend strongly on the π stack conformation. In the present paper, we identify conformations of homogeneous poly-{G}-poly-{C} stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V2, between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G15. The average value of the coupling squared 〈 V2 〉 is found to be 0.0065 eV2. Then we analyze the base-pair and step parameters of the configurations in which V2 is at least an order of magnitude larger than 〈 V2 〉. To obtain more consistent data, ∼65 000 configurations of the (G:C)2 stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures (twist<20°) are of special interest, because the π stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist=30° and 35°, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation (twist38°) seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics

Estimation of electronic coupling in π -stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of Vda because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a π stack, where donor and acceptor are separated by a bridging unit, can be obtained as Ṽ da = (E2 - E1) μ12 Rda + (2 E3 - E1 - E2) 2 μ13 μ23 Rda2, where E1, E2, and E3 are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, μij is the transition dipole moments between the states i and j, and Rda is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model

Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Verification of computed tomographic estimates of cochlear implant array position: A micro-CT and histological analysis

We examine the efficacy two volume spatial registration of pre and postoperative clinical computed tomography (CT) imaging to verify post-operative electrode array placement in cochlear implant (CI) patients. To measure the degree of accuracy with which the composite image predicts in-vivo placement of the array, we replicate the CI surgical process in cadaver heads. Pre-operative, post-operative, micro CT imaging and histology are utilized for verification.

The UK-Canada Agreement on mutual support of missions abroad: loyalty compromised? CEPS Commentary, 18 October 2012

The UK and Canada recently signed a Memorandum of Understanding aimed at allowing the two countries to optimise their respective diplomatic resources by sharing embassy and consulate sites, the joint acquisition, supply and use of services, as well as collaboration on crisis response, consular services, security, diplomatic mail, information management and IT. This CEPS Commentary argues that the MoU on Mutual Support of Missions Abroad runs counter to the spirit of loyal cooperation, in particular in the realm of EU foreign policy. It also raises challenges to coherence, consistency and effectiveness of EU action in policy areas concerning visas, trade and consular protection. Moreover, the agreement may throw a spanner in the works of EU solidarity and the creation of a stronger EU identity, both internally and externally

Solar influences on dynamical coupling between the stratosphere and troposphere

We use a simplified atmospheric general circulation model (AGCM) to investigate the response of the lower atmosphere to thermal perturbations in the lower stratosphere. The results show that generic heating of the lower stratosphere tends to weaken the sub-tropical jets and the tropospheric mean meridional circulations. The positions of the jets, and the extent of the Hadley cells, respond to the distribution of the stratospheric heating, with low latitude heating displacing them poleward, and uniform heating displacing them equatorward. The patterns of response to the low latitude heating are similar to those found to be associated with solar variability in previous observational data analysis, and to the effects of varying solar UV radiation in sophisticated AGCMs. In order to investigate the chain of causality involved in converting the stratospheric thermal forcing to a tropospheric climate signal we conduct an experiment which uses an ensemble of model spin-ups to analyse the time development of the response to an applied stratospheric perturbation. We find that the initial effect of the change in static stability at the tropopause is to reduce the eddy momentum flux convergence in this region. This is followed by a vertical transfer of the momentum forcing anomaly by an anomalous mean circulation to the surface, where it is partly balanced by surface stress anomalies. The unbalanced part drives the evolution of the vertically integrated zonal flow. We conclude that solar heating of the stratosphere may produce changes in the circulation of the troposphere even without any direct forcing below the tropopause. We suggest that the impact of the stratospheric changes on wave propagation is key to the mechanisms involved.

Development of multi-electrode array screening for anticonvulsants in acute rat brain slices

The acute hippocampal brain slice preparation is an important in vitro screening tool for potential anticonvulsants. Application of 4-aminopyridine (4-AP) or removal of external Mg2+ ions induces epileptiform bursting in slices which is analogous to electrical brain activity seen in status epilepticus states. We have developed these epileptiform models for use with multi-electrode arrays (MEAs), allowing recording across the hippocampal slice surface from 59 points. We present validation of this novel approach and analyses using two anticonvulsants, felbamate and phenobarbital, the effects of which have already been assessed in these models using conventional extracellular recordings. In addition to assessing drug effects on commonly described parameters (duration, amplitude and frequency), we describe novel methods using the MEA to assess burst propagation speeds and the underlying frequencies that contribute to the epileptiform activity seen. Contour plots are also used as a method of illustrating burst activity. Finally, we describe hitherto unreported properties of epileptiform bursting induced by 100M4-AP or removal of external Mg2+ ions. Specifically, we observed decreases over time in burst amplitude and increase over time in burst frequency in the absence of additional pharmacological interventions. These MEA methods enhance the depth, quality and range of data that can be derived from the hippocampal slice preparation compared to conventional extracellular recordings. It may also uncover additional modes of action that contribute to anti-epileptiform drug effects