Possible role of interference, protein noise, and sink effects in nonphotochemical quenching in photosynthetic complexes.

We analyze theoretically a simple and consistent quantum mechanical model that reveals the possible role of quantum interference, protein noise, and sink effects in the nonphotochemical quenching (NPQ) in light-harvesting complexes (LHCs). The model consists of a network of five interconnected sites (excitonic states of light-sensitive molecules) responsible for the NPQ mechanism. The model also includes the "damaging" and the dissipative channels. The damaging channel is responsible for production of singlet oxygen and other destructive outcomes. In our model, both damaging and "dissipative" charge transfer channels are described by discrete electron energy levels attached to their sinks, that mimic the continuum part of electron energy spectrum. All five excitonic sites interact with the protein environment that is modeled using a stochastic process. Our approach allowed us to derive the exact and closed system of linear ordinary differential equations for the reduced density matrix and its first momentums. These equations are solved numerically including for strong interactions between the light-sensitive molecules and protein environment. As an example, we apply our model to demonstrate possible contributions of quantum interference, protein noise, and sink effects in the NPQ mechanism in the CP29 minor LHC. The numerical simulations show that using proper combination of quantum interference effects, properties of noise, and sinks, one can significantly suppress the damaging channel. Our findings demonstrate the possible role of interference, protein noise, and sink effects for modeling, engineering, and optimizing the performance of the NPQ processes in both natural and artificial light-harvesting complexes.

Nonlinear dynamics of dipoles in microtubules: Pseudospin model.

We perform a theoretical study of the dynamics of the electric field excitations in a microtubule by taking into consideration the realistic cylindrical geometry, dipole-dipole interactions of the tubulin-based protein heterodimers, the radial electric field produced by the solvent, and a possible degeneracy of energy states of individual heterodimers. The consideration is done in the frame of the classical pseudospin model. We derive the system of nonlinear dynamical partial differential equations of motion for interacting dipoles and the continuum version of these equations. We obtain the solutions of these equations in the form of snoidal waves, solitons, kinks, and localized spikes. Our results will help to achieve a better understanding of the functional properties of microtubules including the motor protein dynamics and the information transfer processes. Our considerations are based on classical dynamics. Some speculations on the role of possible quantum effects are also made.

Decoherence and spin echo in biological systems.

The spin-echo approach is extended to include biocomplexes for which the interaction with dynamical noise, produced by the protein environment, is strong. Significant restoration of the free induction decay signal due to homogeneous (decoherence) and inhomogeneous (dephasing) broadening is demonstrated analytically and numerically for both an individual dimer of interacting chlorophylls and for an ensemble of dimers. Our approach does not require the use of small interaction constants between the electron states and the protein fluctuations. It is based on an exact and closed system of ordinary differential equations that can be easily solved for a wide range of parameters that are relevant for bioapplications.

Role of protein fluctuation correlations in electron transfer in photosynthetic complexes.

We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron (exciton) sites. The fluctuations of the protein environment are modeled by random telegraph processes, which act either collectively (correlated) or independently (uncorrelated) on the electron sites. We derived an exact closed system of first-order linear differential equations with constant coefficients, for the average density matrix elements and for their first moments. Under some conditions, we obtained analytic expressions for the electron transfer rates and found the range of parameters for their applicability by comparing with the exact numerical simulations. We also compared the correlated and uncorrelated regimes and demonstrated numerically that the uncorrelated fluctuations of the protein environment can, under some conditions, either increase or decrease the electron transfer rates.

Sensitivity and entanglement in the avian chemical compass.

The radical pair mechanism can help to explain avian orientation and navigation. Some evidence indicates that the intensity of external magnetic fields plays an important role in avian navigation. In this paper, using a two-stage model, we demonstrate that birds could reasonably detect the directions of geomagnetic fields and gradients of these fields using a yield-based chemical compass that is sensitive enough for navigation. Also, we find that the lifetime of entanglement in this proposed compass is angle dependent and long enough to allow adequate electron transfer between molecules.

Quantum coherence and entanglement in the avian compass.

The radical-pair mechanism is one of two distinct mechanisms used to explain the navigation of birds in geomagnetic fields, however little research has been done to explore the role of quantum entanglement in this mechanism. In this paper we study the lifetime of radical-pair entanglement corresponding to the magnitude and direction of magnetic fields to show that the entanglement lasts long enough in birds to be used for navigation. We also find that the birds appear to not be able to orient themselves directly based on radical-pair entanglement due to a lack of orientation sensitivity of the entanglement in the geomagnetic field. To explore the entanglement mechanism further, we propose a model in which the hyperfine interactions are replaced by local magnetic fields of similar strength. The entanglement of the radical pair in this model lasts longer and displays an angular sensitivity in weak magnetic fields, both of which are not present in previous models.

Stability of the ground state of a harmonic oscillator in a monochromatic wave.

The stability of the ground state of a harmonic oscillator in a monochromatic wave is studied. This model describes, in particular, the dynamics of a cold ion in a linear ion trap, interacting with two laser fields with close frequencies. The stability of the "classical ground state"-the vicinity of the point (x=0,p=0)-is analyzed analytically and numerically. For the quantum case, a method for studying a stability of the quantum ground state is developed, based on the quasienergy representation. It is demonstrated that stability of the ground state may be substantially improved by increasing the resonance number, l, where l=Omega/omega+delta, Omega and omega are, respectively, the wave frequency and the oscillator frequency, l=1,2, em leader, mid R:deltamid R:<1; or by detuning the system from exact resonance, so that delta not equal 0. The influence of a large-amplitude wave (in the presence of chaos) on the stability of the ground state is analyzed for different parameters of the model in both the quantum and classical cases. (c) 2001 American Institute of Physics.

Quantum chaos of an ion trapped in a linear ion trap.

We describe the transition to quantum chaos of an ion trapped in a linear ion trap and interacting with two laser fields. Under the conditions of adiabatic illumination of the upper level of the ion, and when the frequencies of the two laser beams are slightly different, the system is reduced to a quantum linear oscillator interacting with a monochromatic wave. The property of localization over the quantum resonance cells is proposed to exploit in order to facilitate the process of measurement of the probability distribution of an ion on the vibrational levels. In the regime of strong chaos the time-averaged values of the energy and dispersion of energy are computed and compared with the corresponding classical quantities for different values of the perturbation amplitude. In the exact resonance case, the classical analog of the system possesses an infinite inhomogeneous stochastic web. We analyze the quantum dynamics inside the inhomogeneous web. It is shown that the quantum system mimics on average the dynamics of the corresponding classical system. Formation of the quantum resonance cells is illustrated in the case of a finite detuning from the exact resonance, and under increasing of the wave amplitude. The parameters of the model and the initial conditions are close to the real physical situation which can be realized in the system of cold trapped ion perturbed by two lasers fields with close frequencies. (c) 2000 American Institute of Physics.