227 research outputs found
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 . The transport properties are investigated by means of
infinite- 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 . This result is
consistent with recent experiment. We also predict that with decreasing
temperature, the differential conductances at biases anomalously
increase, while the linear conductance descends.Comment: replaced with revised versio
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
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 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
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
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
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
Coherent resonant tunneling in ac fields
We have analyzed the tunneling transmission probability and electronic
current density through resonant heterostructures in the presence of an
external electromagnetic field. In this work, we compare two different models
for a double barrier : In the first case the effect of the external field is
taken into account by spatially dependent AC voltages and in the second one the
electromagnetic field is described in terms of a photon field that irradiates
homogeneously the whole sample. While in the first description the tunneling
takes place mainly through photo sidebands in the case of homogeneous
illumination the main effective tunneling channels correspond to the coupling
between different electronic states due to photon absorption and emission. The
difference of tunneling mechanisms between these configurations is strongly
reflected in the transmission and current density which present very different
features in both cases. In order to analyze these effects we have obtained,
within the Transfer Hamiltonian framework, a general expression for the
transition probability for coherent resonant tunneling in terms of the Green's
function of the system.Comment: 16 pages,Figures available upon request,to appear in Phys.Rev B (15
April 1996
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