Emergence of highly-designable protein-backbone conformations in an off-lattice model

Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino-acid sequences for which they represent the unique ground state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off-lattice model. The highly designable conformations of a chain of 23 amino acids are identified, and found to be remarkably insensitive to model parameters. While some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix-turn-helix motifs, others do not resemble known folds and may be candidates for novel fold design.Comment: 7 figure

Low-temperature transport through a quantum dot between two superconductor leads

We consider a quantum dot coupled to two BCS superconductors with same gap energies $\Delta$. The transport properties are investigated by means of infinite-$U$ noncrossing approximation. In equilibrium density of states, Kondo effect shows up as two sharp peaks around the gap bounds. Application of a finite voltage bias leads these peaks to split, leaving suppressed peaks near the edges of energy gap of each lead. The clearest signatures of the Kondo effect in transport are three peaks in the nonlinear differential conductance: one around zero bias, another two at biases $\pm 2\Delta$. This result is consistent with recent experiment. We also predict that with decreasing temperature, the differential conductances at biases $\pm 2\Delta$ anomalously increase, while the linear conductance descends.Comment: replaced with revised versio

Symmetry and designability for lattice protein models

Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a two-dimensional lattice protein model based on hydrophobicity, we find that those native structures that are encoded by the largest number of different sequences have high symmetry. However only certain symmetries are enhanced, e.g. x/y-mirror symmetry and $180^o$ rotation, while others are suppressed. If it takes a large number of mutations to destabilize the native state of a protein, then, by definition, the state is highly designable. Hence, our findings imply that insensitivity to mutation implies high symmetry. It appears that the relationship between designability and symmetry results because protein substructures are also designable. Native protein folds may therefore be symmetric because they are composed of repeated designable substructures.Comment: 13 pages, 10 figure

Quantum transport through a double Aharonov-Bohm-interferometer in the presence of Andreev reflection

Quantum transport through a double Aharonov-Bohm-interferometer in the presence of Andreev reflection is investigated in terms of the nonequilibrium Green function method with which the reflection current is obtained. Tunable Andreev reflection probabilities depending on the interdot coupling strength and magnetic flux as well are analysised in detail. It is found that the oscillation period of the reflection probability with respect to the magnetic flux for the double interferometer depends linearly on the ratio of two parts magnetic fluxes n, i.e. 2(n+1)pi, while that of a single interferometer is 2pi. The coupling strength not only affects the height and the linewidth of Andreev reflection current peaks vs gate votage but also shifts the peak positions. It is furthermore demonstrated that the Andreev reflection current peaks can be tuned by the magnetic fluxes.Comment: 13 pages, 12 figur

Inelastic resonant tunneling through single molecules and quantum dots: spectrum modification due to nonequilibrium effects

Resonant electron transport through a mesoscopic region (quantum dot or single molecule) with electron-phonon interaction is considered at finite voltage. In this case the standard Landauer-B\"uttiker approach cannot be applied. Using the nonequilibrium Green function method we show that due to a nonequilibrium distribution function of electrons in the mesoscopic region, the inelastic scattering rate and spectral function of the dot become functions of the voltage and have to be calculated self-consistently.Comment: 4 pages, 3 figure

Time-Dependent Spin-Polarized Transport Through a Resonant Tunneling Structure with Multi-Terminal

The spin-dependent transport of the electrons tunneling through a resonant tunneling structure with ferromagnetic multi-terminal under dc and ac fields is explored by means of the nonequilibrium Green function technique. A general formulation for the time-dependent current and the time-averaged current is established. As its application the systems with two and three terminals in noncollinear configurations of the magnetizations under dc and ac biases are investigated, respectively. The asymmetric factor of the relaxation times for the electrons with different spin in the central region is uncovered to bring about various behaviours of the TMR. The present three-terminal device is different from that discussed in literature, which is coined as a spin transistor with source. The current-amplification effect is found. In addition, the time-dependent spin transport for the two-terminal device is studied. It is found that the photonic sidebands provide new channels for the electrons tunneling through the barriers, and give rise to new resonances of the TMR, which is called as the photon-asisted spin-dependent tunneling. The asymmetric factor of the relaxation times is observed to lead to additional resonant peaks besides the photon-asisted resonances.Comment: 32 pages,14 figure

Nonequilibrium Green's-Function Approach to the Suppression of Rectification at Metal--Mott-Insulator Interfaces

Suppression of rectification at metal--Mott-insulator interfaces, which is previously shown by numerical solutions to the time-dependent Schr\"odinger equation and experiments on real devices, is reinvestigated theoretically by nonequilibrium Green's functions. The one-dimensional Hubbard model is used for a Mott insulator. The effects of attached metallic electrodes are incorporated into the self-energy. A scalar potential originating from work-function differences and satisfying the Poisson equation is added to the model. For the electron density, we decompose it into three parts. One is obtained by integrating the local density of states over energy to the midpoint of the electrodes' chemical potentials. The others, obtained by integrating lesser Green's functions, are due to the couplings with the electrodes and correspond to an inflow and an outflow of electrons. In Mott insulators, incoming electrons and holes are extended over the whole system, avoiding further accumulation of charge relative to the case without bias. This induces collective charge transport and results in the suppression of rectification.Comment: 18 pages, Figs. 1(b), 2, and 8 replaced. Corrected typo

On the perturbative expansion of the magnetization in the out-of-equilibrium Kondo model

This paper is concerned with the out-of-equilibrium two-lead Kondo model, considered as a model of a quantum dot in the Kondo regime. We revisit the perturbative expansion of the dot's magnetization, and conclude that, even at order 0 in the Kondo interactions, the magnetization is not given by the usual equilibrium result. We use the Schwinger-Keldysh method to derive a Dyson equation describing the steady state induced by the voltage between the two leads, and thus present the correct procedure for calculating perturbative expansions of steady-state properties of the system.Comment: Minor corrections forgotten in v

Resonant Photon-Assisted Tunneling Through a Double Quantum Dot: An Electron Pump From Spatial Rabi Oscillations

The time average of the fully nonlinear current through a double quantum dot, subject to an arbitrary combination of ac and dc voltages, is calculated exactly using the Keldysh nonequilibrium Green function technique. When driven on resonance, the system functions as an efficient electron pump due to Rabi oscillation between the dots. The pumping current is maximum when the coupling to the leads equals the Rabi frequency.Comment: 6 pages, REVTEX 3.0, 3 postscript figure

Transport through Quantum Dots: Analytic Results from Integrability

Recent experiments have probed quantum dots through transport measurements in the regime where they are described by a two lead Anderson model. In this paper we develop a new method to analytically compute for the first time the corresponding transport properties. This is done by using the exact solvability of the Anderson Hamiltonian, together with a generalization of the Landauer-Buttiker approach to integrable systems. The latter requires proper identification of scattering states, a complex and crucial step in our approach. In the Kondo regime, our results include the zero-field, finite temperature linear response conductance, as well as the zero-temperature, non-equilibrium conductance in an applied Zeeman field.Comment: 5 pages, 3 figure