A quantum chemical investigation of the metal centres in cytochrome c oxidase

Quantum effects are often of key importance for the function of biological systems at molecular level. Cellular respiration, where energy is extracted from the reduction of molecular oxygen to water, is no exception. In this work, the end station of the electron transport chain in mitochondria, cytochrome c oxidase, is investigated using quantum chemical methodology. Cytochrome c oxidase contains two haems, haem a and haem a3. Haem a3, with its copper companion, CuB, is involved in the final reduction of oxygen into water. This binuclear centre receives the necessary electrons from haem a. Haem a, in turn, receives its electrons from a copper ion pair in the vicinity, called CuA. Density functional theory (DFT) has been used to clarify the charge and spin distributions of haem a, as well as changes in these during redox activity. Upon reduction, the added electron is shown to be evenly distributed over the entire haem structure, important for the accommodation of the prosthetic group within the protein. At the same time, the spin distribution of the open-shell oxidised state is more localised to the central iron. The exact spin density distribution has been disputed in the literature, however, different experiments indicating different distributions of the unpaired electron. The apparent contradiction is shown to be due to the false assumption of a unit amount of unpaired electron density; in fact, the oxidised state has about 1.3 unpaired electrons. The validity of the DFT results have been corroborated by wave function based coupled cluster calculations. Point charges, for use in classical force field based simulations, have been parameterised for the four metal centres, using a newly developed methodology. In the procedure, the subsystem for which point charges are to be obtained, is surrounded by an outer region, with the purpose of stabilising the inner region, both electronically and structurally. Finally, the possibility of vibrational promotion of the electron transfer step between haem a and a3 has been investigated. Calculating the full vibrational spectra, at DFT level, of a combined model of the two haems, revealed several normal modes that do shift electron density between the haems. The magnitude of the shift was found to be moderate, at most. The proposed mechanism could have an assisting role in the electron transfer, which still seems to be dominated by electron tunnelling.

Nondiffusive Quantum Transport in a Dynamically Disordered Medium

For a dynamically disordered continuum it is found that the exact quantum mechanical mean square displacement 〈x2(t)〉∼t3, for t→∞. A Gaussian white-noise spectrum is assumed for the random potential. The result differs qualitatively from the diffusive behavior well known for the one-band lattice Hamiltonian, and is understandable in terms of the momentum cutoff inherent in the lattice, simulating a "momentum bath."

The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles N and defining the nonplanarity of the amide unit are correlated approximately by the relation N = -2, while C is small and uncorrelated with . The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (,), in working out polypeptide and protein structures.

Intersoliton forces in weak-coupling quantum field theories

We offer a procedure for evaluating the forces exerted by solitons of weak-coupling field theories on one another. We illustrate the procedure for the kink and the antikink of the two-dimensional φ4 theory. To do this, we construct analytically a static solution of the theory which can be interpreted as a kink and an antikink held a distance R apart. This leads to a definition of the potential energy U(R) for the pair, which is seen to have all the expected features. A corresponding evaluation is also done for U(R) between a soliton and an antisoliton of the sine-Gordon theory. When this U(R) is inserted into a nonrelativistic two-body problem for the pair, it yields a set of bound states and phase shifts. These are found to agree with exact results known for the sine-Gordon field theory in those regions where U(R) is expected to be significant, i.e., when R is large compared to the soliton size. We take this agreement as support that our procedure for defining U(R) yields the correct description of the dynamics of well-separated soliton pairs. An important feature of U(R) is that it seems to give strong intersoliton forces when the coupling constant is small, as distinct from the forces between the ordinary quanta of the theory. We suggest that this is a general feature of a class of theories, and emphasize the possible relevance of this feature to real strongly interacting hadrons.

Unitary Processes with Independent Increments and Representations of Hilbert Tensor Algebras

The aim of this article is to characterize unitary increment process by a quantum stochastic integral representation on symmetric Fock space. Under certain assumptions we have proved its unitary equivalence to a Hudson-Parthasarathy flow.

Simple theoretical analysis of the Einstein's photoemission from quantum confined superlattices

In this paper, we study the Einstein's photoemission from III-V, II-VI, IV-VI and HgTe/CdTe quantum well superlattices (QWSLs) with graded interfaces and quantum well effective mass superlattices in the presence of a quantizing magnetic field on the basis of newly formulated dispersion relations in the respective cases. Besides, the same has been studied from the afore-mentioned quantum dot superlattices and it appears that the photoemission oscillates with increasing carrier degeneracy and quantizing magnetic field in different manners. In addition, the photoemission oscillates with film thickness and increasing photon energy in quantum steps together with the fact that the solution of the Boltzmann transport equation will introduce new physical ideas and new experimental findings under different external conditions. The influence of band structure is apparent from all the figures and we have suggested three applications of the analyses of this paper in the fields of superlattices and microstructures.

Adiabatic quantum computation with a one-dimensional projector Hamiltonian

Adiabatic quantum computation is based on the adiabatic evolution of quantum systems. We analyze a particular class of quantum adiabatic evolutions where either the initial or final Hamiltonian is a one-dimensional projector Hamiltonian on the corresponding ground state. The minimum-energy gap, which governs the time required for a successful evolution, is shown to be proportional to the overlap of the ground states of the initial and final Hamiltonians. We show that such evolutions exhibit a rapid crossover as the ground state changes abruptly near the transition point where the energy gap is minimum. Furthermore, a faster evolution can be obtained by performing a partial adiabatic evolution within a narrow interval around the transition point. These results generalize and quantify earlier works.

Quantum phase analysis of 1D superconducting quantum dot lattice using extended Bose-Hubbard model

We have obtained the quantum phase diagram of a one-dimensional superconducting quantum dot lattice using the extended Bose-Hubbard model for different commensurabilities. We describe the nature of different quantum phases at the charge degeneracy point. We find a direct phase transition from the Mott insulating phase to the superconducting phase for integer band fillings of Cooper pairs. We predict explicitly the presence of two kinds of repulsive Luttinger liquid phases, besides the charge density wave and superconducting phases for half-integer band fillings. We also predict that extended range interactions are necessary to obtain the correct phase boundary of a one-dimensional interacting Cooper system. We have used the density matrix renormalization group method and Abelian bosonization to study our system.

Thermoelectric power in ultrathin films, quantum wires and carbon nanotubes under classically large magnetic field: Simplified theory and relative comparison

We study the thermoelectric power under classically large magnetic field (TPM) in ultrathin films (UFs), quantum wires (QWs) of non-linear optical materials on the basis of a newly formulated electron dispersion law considering the anisotropies of the effective electron masses, the spin-orbit splitting constants and the presence of the crystal field splitting within the framework of k.p formalism. The results of quantum confined III-V compounds form the special cases of our generalized analysis. The TPM has also been studied for quantum confined II-VI, stressed materials, bismuth and carbon nanotubes (CNs) on the basis of respective dispersion relations. It is found taking quantum confined CdGeAs2, InAs, InSb, CdS, stressed n-InSb and Bi that the TPM increases with increasing film thickness and decreasing electron statistics exhibiting quantized nature for all types of quantum confinement. The TPM in CNs exhibits oscillatory dependence with increasing carrier concentration and the signature of the entirely different types of quantum systems are evident from the plots. Besides, under certain special conditions, all the results for all the materials gets simplified to the well-known expression of the TPM for non-degenerate materials having parabolic energy bands, leading to the compatibility test. (C) 2009 Elsevier B.V. All rights reserved.

Quantum Interference in Coherent Molecular Conductance

Coherent electronic transport through individual molecules is crucially sensitive to quantum interference. We investigate the zero-bias and zero-temperature conductance through pi-conjugated annulene molecules weakly coupled to two leads for different source-drain configurations, finding an important reduction for certain transmission channels and for particular geometries as a consequence of destructive quantum interference between states with definite momenta. When translational symmetry is broken by an external perturbation we find an abrupt increase of the conductance through those channels. Previous studies concentrated on the effect at the Fermi energy, where this effect is very small. By analyzing the effect of symmetry breaking on the main transmission channels we find a much larger response thus leading to the possibility of a larger switching of the conductance through single molecules.

Tetragonal bismuth bilayer: A stable and robust quantum spin hall insulator

Topological insulators (TIs) exhibit novel physics with great promise for new devices, but considerable challenges remain to identify TIs with high structural stability and large nontrivial band gap suitable for practical applications. Here we predict by first-principles calculations a two-dimensional (2D) TI, also known as a quantum spin Hall (QSH) insulator, in a tetragonal bismuth bilayer (TB-Bi) structure that is dynamically and thermally stable based on phonon calculations and finite-temperature molecular dynamics simulations. Density functional theory and tight-binding calculations reveal a band inversion among the Bi-p orbits driven by the strong intrinsic spin-orbit coupling, producing a large nontrivial band gap, which can be effectively tuned by moderate strains. The helical gapless edge states exhibit a linear dispersion with a high Fermi velocity comparable to that of graphene, and the QSHphase remains robust on a NaCl substrate. These remarkable properties place TB-Bi among the most promising 2D TIs for high-speed spintronic devices, and the present results provide insights into the intriguing QSH phenomenon in this new Bi structure and offer guidance for its implementation in potential applications.

Power dissipation for systems with junctions of multiple quantum wires

We study power dissipation for systems of multiple quantum wires meeting at a junction, in terms of a current splitting matrix (M) describing the junction. We present a unified framework for studying dissipation for wires with either interacting electrons (i.e., Tomonaga-Luttinger liquid wires with Fermi-liquid leads) or noninteracting electrons. We show that for a given matrix M, the eigenvalues of (MM)-M-T characterize the dissipation, and the eigenvectors identify the combinations of bias voltages which need to be applied to the different wires in order to maximize the dissipation associated with the junction. We use our analysis to propose and study some microscopic models of a dissipative junction which employ the edge states of a quantum Hall liquid. These models realize some specific forms of the M matrix whose entries depends on the tunneling amplitudes between the different edges.

Buckled nano rod - a two state system: quantum effects on its dynamics

We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from the harmonic to the double well regime. The two minima in potential energy curve describe two possible buckled states. Using transition state theory (TST) we have calculated the rate of conversion from one state to other. If the strain epsilon = 4 epsilon c the simple TST rate diverges. We suggest a method to correct this divergence for quantum calculations. We also find that zero point energy contributions can be quite large so that single mode calculations can lead to large errors in the rate.

Thermoelectric Power Under Strong Magnetic Field in Quantum Dots and Quantized Superlattices: Simplified Theory and Relative Comparison

In this paper, we study the thermoelectric power under strong magnetic field (TPSM) in quantum dots (QDs) of nonlinear optical, III-V, II-VI, GaP, Ge, Te, Graphite, PtSb2, zerogap, Lead Germanium Telluride, GaSb, stressed materials, Bismuth, IV-VI, II-V, Zinc and Cadmium diphosphides, Bi2Te3 and Antimony respectively. The TPSM in III-V, II-VI, IV-VI, HgTe/CdTe quantum well superlattices with graded interfaces and effective mass superlattices of the same materials together with the quantum dots of aforementioned superlattices have also been investigated in this context on the basis of respective carrier dispersion laws. It has been found that the TPSM for the said quantum dots oscillates with increasing thickness and decreases with increasing electron concentration in various manners and oscillates with film thickness, inverse quantizing magnetic field and impurity concentration for all types of superlattices with two entirely different signatures of quantization as appropriate in respective cases of the aforementioned quantized structures. The well known expression of the TPSM for wide-gap materials has been obtained as special case for our generalized analysis under certain limiting condition, and this compatibility is an indirect test of our generalized formalism. Besides, we have suggested the experimental method of determining the carrier contribution to elastic constants for nanostructured materials having arbitrary dispersion laws.

Experimental implementation of a three qubit quantum game with corrupt source using nuclear magnetic resonance quantum information processor

In a three player quantum `Dilemma' game each player takes independent decisions to maximize his/her individual gain. The optimal strategy in the quantum version of this game has a higher payoff compared to its classical counterpart. However, this advantage is lost if the initial qubits provided to the players are from a noisy source. We have experimentally implemented the three player quantum version of the `Dilemma' game as described by Johnson, [N.F. Johnson, Phys. Rev. A 63 (2001) 020302(R)] using nuclear magnetic resonance quantum information processor and have experimentally verified that the payoff of the quantum game for various levels of corruption matches the theoretical payoff. (c) 2007 Elsevier Inc. All rights reserved.