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

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

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

Robust Control of Quantum Information

Errors in the control of quantum systems may be classified as unitary, decoherent and incoherent. Unitary errors are systematic, and result in a density matrix that differs from the desired one by a unitary operation. Decoherent errors correspond to general completely positive superoperators, and can only be corrected using methods such as quantum error correction. Incoherent errors can also be described, on average, by completely positive superoperators, but can nevertheless be corrected by the application of a locally unitary operation that ``refocuses'' them. They are due to reproducible spatial or temporal variations in the system's Hamiltonian, so that information on the variations is encoded in the system's spatiotemporal state and can be used to correct them. In this paper liquid-state nuclear magnetic resonance (NMR) is used to demonstrate that such refocusing effects can be built directly into the control fields, where the incoherence arises from spatial inhomogeneities in the quantizing static magnetic field as well as the radio-frequency control fields themselves. Using perturbation theory, it is further shown that the eigenvalue spectrum of the completely positive superoperator exhibits a characteristic spread that contains information on the Hamiltonians' underlying distribution.Comment: 14 pages, 6 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

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. XV. KOI-614b, KOI-206b, and KOI-680b: a massive warm Jupiter orbiting a G0 metallic dwarf and two highly inflated planets with a distant companion around evolved F-type stars

We report the validation and characterization of three new transiting exoplanets using SOPHIE radial velocities: KOI-614b, KOI-206b, and KOI-680b. KOI-614b has a mass of $2.86\pm0.35~{\rm M_{Jup}}$ and a radius of $1.13^{+0.26}_{-0.18}~{\rm R_{Jup}}$, and it orbits a G0, metallic ([Fe/H]=$0.35\pm0.15$) dwarf in 12.9 days. Its mass and radius are familiar and compatible with standard planetary evolution models, so it is one of the few known transiting planets in this mass range to have an orbital period over ten days. With an equilibrium temperature of $T_{eq}=1000 \pm 45$ K, this places KOI-614b at the transition between what is usually referred to as "hot" and "warm" Jupiters. KOI-206b has a mass of $2.82\pm 0.52~{\rm M_{Jup}}$ and a radius of $1.45\pm0.16~{\rm R_{Jup}}$, and it orbits a slightly evolved F7-type star in a 5.3-day orbit. It is a massive inflated hot Jupiter that is particularly challenging for planetary models because it requires unusually large amounts of additional dissipated energy in the planet. On the other hand, KOI-680b has a much lower mass of $0.84\pm0.15~{\rm M_{Jup}}$ and requires less extra-dissipation to explain its uncommonly large radius of $1.99\pm0.18~{\rm R_{Jup}}$. It is one of the biggest transiting planets characterized so far, and it orbits a subgiant F9-star well on its way to the red giant stage, with an orbital period of 8.6 days. With host stars of masses of $1.46\pm0.17~M_{\odot}$ and $1.54 \pm 0.09~M_{\odot}$, respectively, KOI-206b, and KOI-680b are interesting objects for theories of formation and survival of short-period planets around stars more massive than the Sun. For those two targets, we also find signs of a possible distant additional companion in the system