Recoverable One-dimensional Encoding of Three-dimensional Protein Structures

Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it has not been clear whether a given set of 1D structures contains sufficient information for recovering the underlying 3D structure. Here we show that the 3D structure of a protein can be recovered from a set of three types of 1D structures, namely, secondary structure, contact number and residue-wise contact order which is introduced here for the first time. Using simulated annealing molecular dynamics simulations, the structures satisfying the given native 1D structural restraints were sought for 16 proteins of various structural classes and of sizes ranging from 56 to 146 residues. By selecting the structures best satisfying the restraints, all the proteins showed a coordinate RMS deviation of less than 4\AA{} from the native structure, and for most of them, the deviation was even less than 2\AA{}. The present result opens a new possibility to protein structure prediction and our understanding of the sequence-structure relationship.Comment: Corrected title. No Change In Content

Extra-adrenal regeneration of glucocorticoids by 11beta-hydroxysteroid dehydrogenase type 1:physiological regulator and pharmacological target for energy partitioning

The major glucocorticoid in man, cortisol, plays important roles in regulating fuel metabolism, energy partitioning and body fat distribution. In addition to the control of cortisol levels in blood by the hypothalamic-pituitary-adrenal axis, intracellular cortisol levels within target tissues can be controlled by local enzymes. 11Beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1) catalyses the regeneration of active cortisol from inert cortisone, thereby amplifying cortisol levels and glucocorticoid receptor activation in adipose tissue, liver and other tissues. 11Beta-HSD1 is under complex tissue-specific regulation and there is evidence that it adjusts local cortisol concentrations independently of the plasma cortisol concentrations, e.g. in response to changes in diet. In obesity 11beta-HSD1 mRNA and activity in adipose tissue are increased. The mechanism of this up-regulation remains uncertain; polymorphisms in the HSD11B1 gene have been associated with metabolic complications of obesity, including hypertension and type 2 diabetes, but not with obesity per se. Extensive data have been obtained in mice with transgenic over-expression of 11beta-HSD1 in liver and adipocytes, targeted deletion of 11beta-HSD1, and using novel selective 11beta-HSD1 inhibitors; these data support the use of 11beta-HSD1 inhibitors to lower intracellular glucocorticoid levels and treat both obesity and its metabolic complications. Moreover, in human subjects the non-selective 'prototype' inhibitor carbenoxolone enhances insulin sensitivity. Results of clinical studies with novel potent selective 11beta-HSD1 inhibitors are therefore eagerly awaited. The present article focuses on the physiological role of glucocorticoids in regulating energy partitioning, and the evidence that this process is modulated by 11beta-HSD1 in human subjects

Benchmarking quantum control methods on a 12-qubit system

In this letter, we present an experimental benchmark of operational control methods in quantum information processors extended up to 12 qubits. We implement universal control of this large Hilbert space using two complementary approaches and discuss their accuracy and scalability. Despite decoherence, we were able to reach a 12-coherence state (or 12-qubits pseudo-pure cat state), and decode it into an 11 qubit plus one qutrit labeled observable pseudo-pure state using liquid state nuclear magnetic resonance quantum information processors.Comment: 11 pages, 4 figures, to be published in PR

A Note on the correspondence between Qubit Quantum Operations and Special Relativity

We exploit a well-known isomorphism between complex hermitian $2\times 2$ matrices and $\mathbb{R}^4$, which yields a convenient real vector representation of qubit states. Because these do not need to be normalized we find that they map onto a Minkowskian future cone in $\mathbb{E}^{1,3}$, whose vertical cross-sections are nothing but Bloch spheres. Pure states are represented by light-like vectors, unitary operations correspond to special orthogonal transforms about the axis of the cone, positive operations correspond to pure Lorentz boosts. We formalize the equivalence between the generalized measurement formalism on qubit states and the Lorentz transformations of special relativity, or more precisely elements of the restricted Lorentz group together with future-directed null boosts. The note ends with a discussion of the equivalence and some of its possible consequences.Comment: 6 pages, revtex, v3: revised discussio

Principles of Control for Decoherence-Free Subsystems

Decoherence-Free Subsystems (DFS) are a powerful means of protecting quantum information against noise with known symmetry properties. Although Hamiltonians theoretically exist that can implement a universal set of logic gates on DFS encoded qubits without ever leaving the protected subsystem, the natural Hamiltonians that are available in specific implementations do not necessarily have this property. Here we describe some of the principles that can be used in such cases to operate on encoded qubits without losing the protection offered by the DFS. In particular, we show how dynamical decoupling can be used to control decoherence during the unavoidable excursions outside of the DFS. By means of cumulant expansions, we show how the fidelity of quantum gates implemented by this method on a simple two-physical-qubit DFS depends on the correlation time of the noise responsible for decoherence. We further show by means of numerical simulations how our previously introduced "strongly modulating pulses" for NMR quantum information processing can permit high-fidelity operations on multiple DFS encoded qubits in practice, provided that the rate at which the system can be modulated is fast compared to the correlation time of the noise. The principles thereby illustrated are expected to be broadly applicable to many implementations of quantum information processors based on DFS encoded qubits.Comment: 12 pages, 7 figure

A Study of Quantum Error Correction by Geometric Algebra and Liquid-State NMR Spectroscopy

Quantum error correcting codes enable the information contained in a quantum state to be protected from decoherence due to external perturbations. Applied to NMR, quantum coding does not alter normal relaxation, but rather converts the state of a ``data'' spin into multiple quantum coherences involving additional ancilla spins. These multiple quantum coherences relax at differing rates, thus permitting the original state of the data to be approximately reconstructed by mixing them together in an appropriate fashion. This paper describes the operation of a simple, three-bit quantum code in the product operator formalism, and uses geometric algebra methods to obtain the error-corrected decay curve in the presence of arbitrary correlations in the external random fields. These predictions are confirmed in both the totally correlated and uncorrelated cases by liquid-state NMR experiments on 13C-labeled alanine, using gradient-diffusion methods to implement these idealized decoherence models. Quantum error correction in weakly polarized systems requires that the ancilla spins be prepared in a pseudo-pure state relative to the data spin, which entails a loss of signal that exceeds any potential gain through error correction. Nevertheless, this study shows that quantum coding can be used to validate theoretical decoherence mechanisms, and to provide detailed information on correlations in the underlying NMR relaxation dynamics.Comment: 33 pages plus 6 figures, LaTeX article class with amsmath & graphicx package

SOPHIE velocimetry of Kepler transit candidates XI. Kepler-412 system: probing the properties of a new inflated hot Jupiter

We confirm the planetary nature of Kepler-412b, listed as planet candidate KOI-202 in the Kepler catalog, thanks to our radial velocity follow-up program of Kepler-released planet candidates, which is on going with the SOPHIE spectrograph. We performed a complete analysis of the system by combining the Kepler observations from Q1 to Q15, to ground-based spectroscopic observations that allowed us to derive radial velocity measurements, together with the host star parameters and properties. We also analyzed the light curve to derive the star's rotation period and the phase function of the planet, including the secondary eclipse. We found the planet has a mass of 0.939 $\pm$ 0.085 M$_{Jup}$ and a radius of 1.325 $\pm$ 0.043 R$_{Jup}$ which makes it a member of the bloated giant subgroup. It orbits its G3 V host star in 1.72 days. The system has an isochronal age of 5.1 Gyr, consistent with its moderate stellar activity as observed in the Kepler light curve and the rotation of the star of 17.2 $\pm$ 1.6 days. From the detected secondary, we derived the day side temperature as a function of the geometric albedo and estimated the geometrical albedo, Ag, is in the range 0.094 to 0.013. The measured night side flux corresponds to a night side brightness temperature of 2154 $\pm$ 83 K, much greater than what is expected for a planet with homogeneous heat redistribution. From the comparison to star and planet evolution models, we found that dissipation should operate in the deep interior of the planet. This modeling also shows that despite its inflated radius, the planet presents a noticeable amount of heavy elements, which accounts for a mass fraction of 0.11 $\pm$ 0.04.Comment: 11 pages, 9 figure

A Method for Modeling Decoherence on a Quantum Information Processor

We develop and implement a method for modeling decoherence processes on an N-dimensional quantum system that requires only an $N^2$-dimensional quantum environment and random classical fields. This model offers the advantage that it may be implemented on small quantum information processors in order to explore the intermediate regime between semiclassical and fully quantum models. We consider in particular $\sigma_z\sigma_z$ system-environment couplings which induce coherence (phase) damping, though the model is directly extendable to other coupling Hamiltonians. Effective, irreversible phase-damping of the system is obtained by applying an additional stochastic Hamiltonian on the environment alone, periodically redressing it and thereby irreversibliy randomizing the system phase information that has leaked into the environment as a result of the coupling. This model is exactly solvable in the case of phase-damping, and we use this solution to describe the model's behavior in some limiting cases. In the limit of small stochastic phase kicks the system's coherence decays exponentially at a rate which increases linearly with the kick frequency. In the case of strong kicks we observe an effective decoupling of the system from the environment. We present a detailed implementation of the method on an nuclear magnetic resonance quantum information processor.Comment: 12 pages, 9 figure

Experimental Implementation of Logical Bell State Encoding

Liquid phase NMR is a general purpose test-bed for developing methods of coherent control relevant to quantum information processing. Here we extend these studies to the coherent control of logical qubits and in particular to the unitary gates necessary to create entanglement between logical qubits. We report an experimental implementation of a conditional logical gate between two logical qubits that are each in decoherence free subspaces that protect the quantum information from fully correlated dephasing.Comment: 9 Pages, 5 Figure