A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

AbstractThe formation of water chains in cytochrome c oxidase (CcO) is studied by molecular dynamics (MD). Focus is on water chains in the K channel that can supply a proton to the binuclear center (the heme a3 Fe/CuB region), the site of O2 reduction. By assessing the presence of chains of any length on a short time scale (0.1 ps), a view of the kinds of chains and their persistence is obtained. Chains from the entry of the channel on the inner membrane to Thr359 (Rhodobacter sphaeroides numbering) are often present but are blocked at that point until a rotation of the Thr359 side chain occurs, permitting formation of chains from Thr359 towards the binuclear center. No continuous hydrogen-bonded water chains are found connecting Thr359 and the binuclear center. Instead, waters hydrogen bond from Thr359 to the hydroxyl of the heme a3 farnesyl and then continue to the binuclear center via Tyr288, which has been identified as a source of a proton for O2 reduction. Three hydrogen-bonded waters are found to be present in the binuclear center after a sufficiently long simulation time. One is ligated to the CuB and could be associated with a water (or hydroxyl) identified in the crystal structure as the fourth ligand of CuB. The water hydrogen-bonded to the hydroxyl of Tyr288 is extremely persistent and well positioned to participate in O2 reduction. The third water is located where O2 is often suggested to reside in mechanistic studies of O2 reduction

Dynamics of spin-2 Bose condensate driven by external magnetic fields

Dynamic response of the F=2 spinor Bose-Einstein condensate (BEC) under the influence of external magnetic fields is studied. A general formula is given for the oscillation period to describe population transfer from the initial polar state to other spin states. We show that when the frequency and the reduced amplitude of the longitudinal magnetic field are related in a specific manner, the population of the initial spin-0 state will be dynamically localized during time evolution. The effects of external noise and nonlinear spin exchange interaction on the dynamics of the spinor BEC are studied. We show that while the external noise may eventually destroy the Rabi oscillations and dynamic spin localization, these coherent phenomena are robust against the nonlinear atomic interaction.Comment: 16 pages, 7 figures. accepted by Phys. Rev.

Heating and decoherence suppression using decoupling techniques

We study the application of decoupling techniques to the case of a damped vibrational mode of a chain of trapped ions, which can be used as a quantum bus in linear ion trap quantum computers. We show that vibrational heating could be efficiently suppressed using appropriate ``parity kicks''. We also show that vibrational decoherence can be suppressed by this decoupling procedure, even though this is generally more difficult because the rate at which the parity kicks have to applied increases with the effective bath temperature.Comment: 13 pages, 5 figures. Typos corrected, references adde

Electron energy loss and induced photon emission in photonic crystals

The interaction of a fast electron with a photonic crystal is investigated by solving the Maxwell equations exactly for the external field provided by the electron in the presence of the crystal. The energy loss is obtained from the retarding force exerted on the electron by the induced electric field. The features of the energy loss spectra are shown to be related to the photonic band structure of the crystal. Two different regimes are discussed: for small lattice constants $a$ relative to the wavelength of the associated electron excitations $\lambda$, an effective medium theory can be used to describe the material; however, for $a\sim\lambda$ the photonic band structure plays an important role. Special attention is paid to the frequency gap regions in the latter case.Comment: 12 pages, 7 figure

Statistical Theory of Spin Relaxation and Diffusion in Solids

A comprehensive theoretical description is given for the spin relaxation and diffusion in solids. The formulation is made in a general statistical-mechanical way. The method of the nonequilibrium statistical operator (NSO) developed by D. N. Zubarev is employed to analyze a relaxation dynamics of a spin subsystem. Perturbation of this subsystem in solids may produce a nonequilibrium state which is then relaxed to an equilibrium state due to the interaction between the particles or with a thermal bath (lattice). The generalized kinetic equations were derived previously for a system weakly coupled to a thermal bath to elucidate the nature of transport and relaxation processes. In this paper, these results are used to describe the relaxation and diffusion of nuclear spins in solids. The aim is to formulate a successive and coherent microscopic description of the nuclear magnetic relaxation and diffusion in solids. The nuclear spin-lattice relaxation is considered and the Gorter relation is derived. As an example, a theory of spin diffusion of the nuclear magnetic moment in dilute alloys (like Cu-Mn) is developed. It is shown that due to the dipolar interaction between host nuclear spins and impurity spins, a nonuniform distribution in the host nuclear spin system will occur and consequently the macroscopic relaxation time will be strongly determined by the spin diffusion. The explicit expressions for the relaxation time in certain physically relevant cases are given.Comment: 41 pages, 119 Refs. Corrected typos, added reference

A review of techniques for parameter sensitivity analysis of environmental models

Mathematical models are utilized to approximate various highly complex engineering, physical, environmental, social, and economic phenomena. Model parameters exerting the most influence on model results are identified through a ‘sensitivity analysis’. A comprehensive review is presented of more than a dozen sensitivity analysis methods. This review is intended for those not intimately familiar with statistics or the techniques utilized for sensitivity analysis of computer models. The most fundamental of sensitivity techniques utilizes partial differentiation whereas the simplest approach requires varying parameter values one-at-a-time. Correlation analysis is used to determine relationships between independent and dependent variables. Regression analysis provides the most comprehensive sensitivity measure and is commonly utilized to build response surfaces that approximate complex models.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42691/1/10661_2004_Article_BF00547132.pd