263 research outputs found
Digital Cavities and Their Potential Applications
The concept of a digital cavity is presented. The functionality of a tunable
radio-frequency/microwave cavity with unrestricted Q-factor is implemented. The
theoretical aspects of the cavity and its potential applications in high
resolution spectroscopy and synchronization of clocks together with examples in
signal processing and data acquisition are discussed
High Precision Measurements Using High Frequency Signals
Generalized lock-in amplifiers use digital cavities with Q-factors as high as
5X10^8. In this letter, we show that generalized lock-in amplifiers can be used
to analyze microwave (giga-hertz) signals with a precision of few tens of
hertz. We propose that the physical changes in the medium of propagation can be
measured precisely by the ultra-high precision measurement of the signal. We
provide evidence to our proposition by verifying the Newton's law of cooling by
measuring the effect of change in temperature on the phase and amplitude of the
signals propagating through two calibrated cables. The technique could be used
to precisely measure different physical properties of the propagation medium,
for example length, resistance, etc. Real time implementation of the technique
can open up new methodologies of in-situ virtual metrology in material design
Determination of Fluorescence Polarization and Absorption Anisotropy in Molecular Complexes Having Threefold Rotational Symmetry
The current work concerns investigation of the polarization properties of complex molecular ensembles exhibiting threefold (C3) rotational symmetry, particularly with regard to the interplay between their structure and dynamics of internal energy transfer. We assume that the molecules or chromophores in such complexes possess strongly overlapped spectra both for absorption and fluorescence. Such trimeric structures are widely found in biological preparations, as for example the trimer of C-phycocyanin (C-PC). Higher order aggregates, e.g. hex-amers and three-hexamer rods, are also investigated and compared with the trimer case. The theory addresses both steady-state and 8-pulse excitation and establishes some links between them. Monochromophoric, bichro-mophoric and trichromophoric molecular complexes are individually examined. For steady-state excitation, analytical formulas are reported for the degree of fluorescence polarization and absorption anisotropy. It is shown that the polarization is dependent on the chromophore inclination relative to the symmetry axis, the relative efficiencies of absorption and fluorescence by chromophores of different spectral types, and the rates of energy equilibration. To assess the validity of the theory, it has been applied to C-PC aggregates. Here it was found that different C-PC aggregates provide practically identical polarization response. For S-pulse excitation we give analytical formulas for determination of the fluorescence depolarization, and also the depolarization associated with absorption recovery, both for a monochromophoric trimer and some particular cases of bichromophoric trimer. More complicated systems are analyzed by computer modeling. Thus it transpires that the initial polarization anisotropy r(t = 0) takes the value 0.4 for all considered aggregates; the long-time limit r(t ââ) has about the same value as is associated with steady-state excitation. We also show that with steady-state excitation the degree of fluorescence polarization is practically equal for various C3 aggregates of C-PC, and that the major factor determining the polarization is the chromophore orientation relative to the symmetry axis
Energy Relaxation in Nonlinear One-Dimensional Lattices
We study energy relaxation in thermalized one-dimensional nonlinear arrays of
the Fermi-Pasta-Ulam type. The ends of the thermalized systems are placed in
contact with a zero-temperature reservoir via damping forces. Harmonic arrays
relax by sequential phonon decay into the cold reservoir, the lower frequency
modes relaxing first. The relaxation pathway for purely anharmonic arrays
involves the degradation of higher-energy nonlinear modes into lower energy
ones. The lowest energy modes are absorbed by the cold reservoir, but a small
amount of energy is persistently left behind in the array in the form of almost
stationary low-frequency localized modes. Arrays with interactions that contain
both a harmonic and an anharmonic contribution exhibit behavior that involves
the interplay of phonon modes and breather modes. At long times relaxation is
extremely slow due to the spontaneous appearance and persistence of energetic
high-frequency stationary breathers. Breather behavior is further ascertained
by explicitly injecting a localized excitation into the thermalized array and
observing the relaxation behavior
Excitonic Funneling in Extended Dendrimers with Non-Linear and Random Potentials
The mean first passage time (MFPT) for photoexcitations diffusion in a
funneling potential of artificial tree-like light-harvesting antennae
(phenylacetylene dendrimers with generation-dependent segment lengths) is
computed. Effects of the non-linearity of the realistic funneling potential and
slow random solvent fluctuations considerably slow down the center-bound
diffusion beyond a temperature-dependent optimal size. Diffusion on a
disordered Cayley tree with a linear potential is investigated analytically. At
low temperatures we predict a phase in which the MFPT is dominated by a few
paths.Comment: 4 pages, 4 figures, To be published in Phys. Rev. Let
Quantum entanglement in photosynthetic light harvesting complexes
Light harvesting components of photosynthetic organisms are complex, coupled,
many-body quantum systems, in which electronic coherence has recently been
shown to survive for relatively long time scales despite the decohering effects
of their environments. Within this context, we analyze entanglement in
multi-chromophoric light harvesting complexes, and establish methods for
quantification of entanglement by presenting necessary and sufficient
conditions for entanglement and by deriving a measure of global entanglement.
These methods are then applied to the Fenna-Matthews-Olson (FMO) protein to
extract the initial state and temperature dependencies of entanglement. We show
that while FMO in natural conditions largely contains bipartite entanglement
between dimerized chromophores, a small amount of long-range and multipartite
entanglement exists even at physiological temperatures. This constitutes the
first rigorous quantification of entanglement in a biological system. Finally,
we discuss the practical utilization of entanglement in densely packed
molecular aggregates such as light harvesting complexes.Comment: 14 pages, 7 figures. Improved presentation, published versio
Full characterization of vibrational coherence in a porphyrin chromophore by two-dimensional electronic spectroscopy
In this work we present experimental and calculated two-dimensional electronic spectra for a 5,15-bisalkynyl porphyrin chromophore. The lowest energy electronic Qy transition couples mainly to a single 380 cmâ1 vibrational mode. The two-dimensional electronic spectra reveal diagonal and cross peaks which oscillate as a function of population time. We analyze both the amplitude and phase distribution of this main vibronic transition as a function of excitation and detection frequencies. Even though Feynman diagrams provide a good indication of where the amplitude of the oscillating components are located in the excitation-detection plane, other factors also affect this distribution. Specifically, the oscillation corresponding to each Feynman diagram is expected to have a phase that is a function of excitation and detection frequencies. Therefore, the overall phase of the experimentally observed oscillation will reflect this phase dependence. Another consequence is that the overall oscillation amplitude can show interference patterns resulting from overlapping contributions from neighboring Feynman diagrams. These observations are consistently reproduced through simulations based on third order perturbation theory coupled to a spectral density described by a Brownian oscillator model
Nanoscale Confinement and Fluorescence Effects of Bacterial Light Harvesting Complex LH2 in Mesoporous Silicas
Many key chemical and biochemical reactions, particularly in living cells, take place in confined space at the mesoscopic scale. Toward understanding of physicochemical nature of biomacromolecules confined in nanoscale space, in this work we have elucidated fluorescence effects of a light harvesting complex LH2 in nanoscale chemical environments. Mesoporous silicas (SBA-15 family) with different shapes and pore sizes were synthesized and used to create nanoscale biomimetic environments for molecular confinement of LH2. A combination of UV-vis absorption, wide-field fluorescence microscopy, and in situ ellipsometry supports that the LH2 complexes are located inside the silica nanopores. Systematic fluorescence effects were observed and depend on degree of space confinement. In particular, the temperature dependence of the steady-state fluorescence spectra was analyzed in detail using condensed matter band shape theories. Systematic electronic-vibrational coupling differences in the LH2 transitions between the free and confined states are found, most likely responsible for the fluorescence effects experimentally observed
Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study
The dynamics of pigment-pigment and pigment-protein interactions in
light-harvesting complexes is studied with a novel approach which combines
molecular dynamics (MD) simulations with quantum chemistry (QC) calculations.
The MD simulations of an LH-II complex, solvated and embedded in a lipid
bilayer at physiological conditions (with total system size of 87,055 atoms)
revealed 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. The fluctuations of pigment (B850
BChl) excitation energies, as a function of time, were determined via ab initio
QC calculations based on the geometries that emerged from the MD simulations.
From the results of these calculations we constructed a time-dependent
Hamiltonian of the B850 exciton system from which we determined the linear
absorption spectrum. Finally, a polaron model is introduced to describe quantum
mechanically both the excitonic and vibrational (phonon) degrees of freedom.
The exciton-phonon coupling that enters into the polaron model, and the
corresponding phonon spectral function are derived from the MD/QC simulations.
It is demonstrated that, in the framework of the polaron model, the absorption
spectrum of the B850 excitons can be calculated from the autocorrelation
function of the excitation energies of individual BChls, which is readily
available from the combined MD/QC simulations. The obtained result is in good
agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF
file of the paper is available at
http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd
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