Fast Quantum Search Algorithms in Protein Sequence Comparison - Quantum Biocomputing

Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case - namely where the database forms a complete set of states over the 2^m basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(sqrt{N}) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where the database may contain repeat sequences, and may not necessarily contain an exact match to the sample sequence. In terms of minimizing the Hamming distance between the sample sequence and the database subsequences the algorithm finds an optimal alignment, in O(sqrt{N}) steps, by employing an extension of Grover's algorithm, due to Boyer, Brassard, Hoyer and Tapp for the case when the number of matches is not a priori known.Comment: LaTeX, 5 page

Fast Shocks From Magnetic Reconnection Outflows

Magnetic reconnection is commonly perceived to drive flow and particle acceleration in flares of solar, stellar, and astrophysical disk coronae but the relative roles of different acceleration mecha- nisms in a given reconnection environment are not well understood. We show via direct numerical simulations that reconnection outflows produce weak fast shocks, when conditions for fast recon- nection are met and the outflows encounter an obstacle. The associated compression ratios lead to a Fermi acceleration particle spectrum that is significantly steeper than the strong fast shocks commonly studied, but consistent with the demands of solar flares. While this is not the only acceleration mechanism operating in a reconnection environment, it is plausibly a ubiquitous one

Lossless quantum data compression and variable-length coding

In order to compress quantum messages without loss of information it is necessary to allow the length of the encoded messages to vary. We develop a general framework for variable-length quantum messages in close analogy to the classical case and show that lossless compression is only possible if the message to be compressed is known to the sender. The lossless compression of an ensemble of messages is bounded from below by its von-Neumann entropy. We show that it is possible to reduce the number of qbits passing through a quantum channel even below the von-Neumann entropy by adding a classical side-channel. We give an explicit communication protocol that realizes lossless and instantaneous quantum data compression and apply it to a simple example. This protocol can be used for both online quantum communication and storage of quantum data.Comment: 16 pages, 5 figure

Incomplete quantum process tomography and principle of maximal entropy

The main goal of this paper is to extend and apply the principle of maximum entropy (MaxEnt) to incomplete quantum process estimation tasks. We will define a so-called process entropy function being the von Neumann entropy of the state associated with the quantum process via Choi-Jamiolkowski isomorphism. It will be shown that an arbitrary process estimation experiment can be reformulated in a unified framework and MaxEnt principle can be consistently exploited. We will argue that the suggested choice for the process entropy satisfies natural list of properties and it reduces to the state MaxEnt principle, if applied to preparator devices.Comment: 8 pages, comments welcome, references adde

Unified model for vortex-string network evolution

We describe and numerically test the velocity-dependent one-scale (VOS) string evolution model, a simple analytic approach describing a string network with the averaged correlation length and velocity. We show that it accurately reproduces the large-scale behaviour (in particular the scaling laws) of numerical simulations of both Goto-Nambu and field theory string networks. We explicitly demonstrate the relation between the high-energy physics approach and the damped and non-relativistic limits which are relevant for condensed matter physics. We also reproduce experimental results in this context and show that the vortex-string density is significantly reduced by loop production, an effect not included in the usual `coarse-grained' approach.Comment: 5 pages; v2: cosmetic changes, version to appear in PR

Cryogenic-coolant He4-superconductor dynamic and static interactions

A composite superconducting material (NbTi-Cu) was evaluated with emphasis on post quench solid cooling interaction regimes. The quasi-steady runs confirm the existence of a thermodynamic limiting thickness for insulating coatings. Two distinctly different post quench regimes of coated composites are shown to relate to the limiting thickness. Only one regime,, from quench onset to the peak value, revealed favorable coolant states, in particular in He2. Transient recovery shows favorable recovery times from this post quench regime (not drastically different from bare conductors) for both single coated specimens and a coated conductor bundle

Reconstruction of Liouvillian Superoperators

We show how to determine (reconstruct) a master equation governing the time evolution of an open quantum system. We present a general algorithm for the reconstruction of the corresponding Liouvillian superoperators. Dynamics of a two-level atom in various environments is discussed in detail.Comment: 4 pages, revtex, 1 eps figure, accepted for publication in Phys. Rev.

Validating IoT Devices with Rate-Based Session Types

We develop a session types based framework for implementing and validating rate-based message passing systems in Internet of Things (IoT) domains. To model the indefinite repetition present in many embedded and IoT systems, we introduce a timed process calculus with a periodic recursion primitive. This allows us to model rate-based computations and communications inherent to these application domains. We introduce a definition of rate based session types in a binary session types setting and a new compatibility relationship, which we call rate compatibility. Programs which type check enjoy the standard session types guarantees as well as rate error freedom --- meaning processes which exchanges messages do so at the same rate. Rate compatibility is defined through a new notion of type expansion, a relation that allows communication between processes of differing periods by synthesizing and checking a common superperiod type. We prove type preservation and rate error freedom for our system, and show a decidable method for type checking based on computing superperiods for a collection of processes. We implement a prototype of our type system including rate compatibility via an embedding into the native type system of Rust. We apply this framework to a range of examples from our target domain such as Android software sensors, wearable devices, and sound processing

The role of preparation in quantum process tomography

In a recent letter one of us pointed out how differences in preparation procedures for quantum experiments can lead to non-trivial differences in the results of the experiment. The difference arise from the initial correlations between the system and environment. Therefore, any quantum experiment that is prone to the influences from the environment must be prepared carefully. In this paper, we study quantum process tomography in light of this. We suggest several experimental setups, where preparation of initial state plays a role on the final outcome of the experiment. We show that by studying the linearity and the positivity of the resulting maps the experimenter can determine the nature of the initial correlations between the system and the environment.Comment: 11 pages, 4 fig