The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of lightharvesting complexes was performed on an 87,055 atom system comprised of an LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. The simulation provided information about the extent and timescales of geometrical deformations of pigment and protein residues at physiological temperatures, revealing also a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. For each of the 16 B850 BChls we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 bacteriochlorophyll ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption spectrum of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained result is found to be in good agreement with the experimentally measured absorption spectrum. PACS number(s): 87.15. Aa, 87.15.Mi, 87.16.Ac

We propose a theoretical description of the superconducting state of under-to overdoped cuprates, based on the short coherence length of these materials and the associated strong pairing fluctuations. The calculated Tc and the zero temperature excitation gap ∆(0), as a function of hole concentration x, are in semi-quantitative agreement with experiment. Although the ratio Tc/∆(0) has a strong x dependence, different from the universal BCS value, and ∆(T ) deviates significantly from the BCS prediction, we obtain, quite remarkably, quasi-universal behavior, for the normalized superfluid density ρs(T )/ρs(0) and the Josephson critical current Ic(T )/Ic (0), as a function of T /Tc. While experiments on ρs(T ) are consistent with these results, future measurements on Ic(T ) are needed to test this prediction.PACS numbers: 74.20.-z, 74.25.-q, 74.62.-c, 74.72.-h cond-mat/9807414

We show that, under certain conditions, the low temperature behavior of the magnetic penetration depth λ(T ) of a pure d-wave superconductor is determined by nonlocal electrodynamics and, contrary to the general belief, the deviation ∆λ(T ) = λ(T ) − λ(0) is proportional to T 2 and not T . We predict that the ∆λ(T ) ∝ T 2 dependence, due to nonlocality, should be observable experimentally in nominally clean high-Tc superconductors below a crossover temperature T * = (ξo/λo) ∆o ∼ 1K. Possible complications due to impurities, surface quality and crystal axes orientation are discussed.

In this paper we study the BCS Bose Einstein condensation (BEC) crossover scenario within the superconducting state, using a T-matrix approach which yields the ground state proposed by Leggett. Here we extend this ground state analysis to finite temperatures T and interpret the resulting physics. We find two types of bosonic-like excitations of the system: long lived, incoherent pair excitations and collective modes of the superconducting order parameter, which have different dynamics. Using a gauge invariant formalism, this paper addresses their contrasting behavior as a function of T and superconducting coupling constant g. At a more physical level, our paper emphasizes how, at finite T , BCS-BEC approaches introduce an important parameter ∆ 2 pg = ∆ 2 − ∆ 2 sc into the description of superconductivity. This parameter is governed by the pair excitations and is associated with particle-hole asymmetry effects which are important for sufficiently large g. In the fermionic regime, ∆ 2 pg represents the difference between the square of the excitation gap ∆ 2 and that of the superconducting order parameter ∆ 2 sc . The parameter ∆ 2 pg , which is necessarily zero in the BCS (mean field) limit increases monotonically with the strength of the attractive interaction g. It follows that there is a significant physical distinction between this BCS-BEC crossover approach (in which g is the essential variable which determines ∆pg) and the widely discussed (Coulomb-modulated) phase fluctuation scenario in which the plasma frequency is the tuning parameter. Finally, we emphasize that in the strong coupling limit, there are important differences between the composite bosons which arise in crossover theories, and the usual bosons of the (interacting) Bose liquid. Because of constraints imposed on the fermionic excitation gap and chemical potential, in crossover theories, the fermionic degrees of freedom can never be fully removed from consideration.

We use a long, all-atom molecular-dynamics ͑MD͒ simulation combined with theoretical modeling to investigate the dynamics of selected lipid atoms and lipid molecules in a hydrated diyristoyl-phosphatidylcholine lipid bilayer. From the analysis of a 0.1 s MD trajectory, we find that the time evolution of the mean-square displacement, ͓͗␦r͑t͔͒ 2 ͘, of lipid atoms and molecules exhibits three well-separated dynamical regions: ͑i͒ ballistic, with ͓͗␦r͑t͔͒ 2 ͘ϳt 2 for t Շ 10 fs; ͑ii͒ subdiffusive, with ͓͗␦r͑t͔͒ 2 ͘ϳt ␤ with ␤ Ͻ 1 for 10 psՇ t Շ 10 ns; and ͑iii͒ Fickian diffusion, with ͓͗␦r͑t͔͒ 2 ͘ϳt for t տ 30 ns. We propose a memory-function approach for calculating ͓͗␦r͑t͔͒ 2 ͘ over the entire time range extending from the ballistic to the Fickian diffusion regimes. The results are in very good agreement with the ones from the MD simulations. We also examine the implications of the presence of the subdiffusive dynamics of lipids on the self-intermediate scattering function and the incoherent dynamic structure factor measured in neutron-scattering experiments.