Domain discovery method for topological profile searches in protein structures

We describe a method for automated domain discovery for topological profile searches in protein structures. The method is used in a system TOPStructure for fast prediction of CATH classification for protein structures (given as PDB files). It is important for profile searches in multi-domain proteins, for which the profile method by itself tends to perform poorly. We also present an O(C(n)k +nk2) time algorithm for this problem, compared to the O(C(n)k +(nk)2) time used by a trivial algorithm (where n is the length of the structure, k is the number of profiles and C(n) is the time needed to check for a presence of a given motif in a structure of length n). This method has been developed and is currently used for TOPS representations of protein structures and prediction of CATH classification, but may be applied to other graph-based representations of protein or RNA structures and/or other prediction problems. A protein structure prediction system incorporating the domain discovery method is available at http://bioinf.mii.lu.lv/tops/

Solar Orbiter: Exploring the Sun-heliosphere connection

The heliosphere represents a uniquely accessible domain of space, where fundamental physical processes common to solar, astrophysical and laboratory plasmas can be studied under conditions impossible to reproduce on Earth and unfeasible to observe from astronomical distances. Solar Orbiter, the first mission of ESA's Cosmic Vision 2015-2025 programme, will address the central question of heliophysics: How does the Sun create and control the heliosphere? In this paper, we present the scientific goals of the mission and provide an overview of the mission implementation.Comment: 52 pages, 21 figures, 125 references; accepted for publication in Solar Physic

Non-equilibrium Lorentz gas on a curved space

The periodic Lorentz gas with external field and iso-kinetic thermostat is equivalent, by conformal transformation, to a billiard with expanding phase-space and slightly distorted scatterers, for which the trajectories are straight lines. A further time rescaling allows to keep the speed constant in that new geometry. In the hyperbolic regime, the stationary state of this billiard is characterized by a phase-space contraction rate, equal to that of the iso-kinetic Lorentz gas. In contrast to the iso-kinetic Lorentz gas where phase-space contraction occurs in the bulk, the phase-space contraction rate here takes place at the periodic boundaries

Hysteresis loops of magnetic thin films with perpendicular anisotropy

We model the magnetization of quasi two-dimensional systems with easy perpendicular (z-)axis anisotropy upon change of external magnetic field along z. The model is derived from the Landau-Lifshitz-Gilbert equation for magnetization evolution, written in closed form in terms of the z component of the magnetization only. The model includes--in addition to the external field--magnetic exchange, dipolar interactions and structural disorder. The phase diagram in the disorder/interaction strength plane is presented, and the different qualitative regimes are analyzed. The results compare very well with observed experimental hysteresis loops and spatial magnetization patterns, as for instance for the case of Co-Pt multilayers.Comment: 8 pages, 8 figure

Non-Volatile Magnonic Logic Circuits Engineering

We propose a concept of magnetic logic circuits engineering, which takes an advantage of magnetization as a computational state variable and exploits spin waves for information transmission. The circuits consist of magneto-electric cells connected via spin wave buses. We present the result of numerical modeling showing the magneto-electric cell switching as a function of the amplitude as well as the phase of the spin wave. The phase-dependent switching makes it possible to engineer logic gates by exploiting spin wave buses as passive logic elements providing a certain phase-shift to the propagating spin waves. We present a library of logic gates consisting of magneto-electric cells and spin wave buses providing 0 or p phase shifts. The utilization of phases in addition to amplitudes is a powerful tool which let us construct logic circuits with a fewer number of elements than required for CMOS technology. As an example, we present the design of the magnonic Full Adder Circuit comprising only 5 magneto-electric cells. The proposed concept may provide a route to more functional wave-based logic circuitry with capabilities far beyond the limits of the traditional transistor-based approach

An investigation of the time series of visibility and precipitation intensity fluctuations

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Meteorology, 1961.Includes bibliographical references (leaf 91).by Gilbert D. Brinckerhoff and Denis G. Dartt.M.S

A model checking approach to the parameter estimation of biochemical pathways

Model checking has historically been an important tool to verify models of a wide variety of systems. Typically a model has to exhibit certain properties to be classed ‘acceptable’. In this work we use model checking in a new setting; parameter estimation. We characterise the desired behaviour of a model in a temporal logic property and alter the model to make it conform to the property (determined through model checking). We have implemented a computational system called MC2(GA) which pairs a model checker with a genetic algorithm. To drive parameter estimation, the fitness of set of parameters in a model is the inverse of the distance between its actual behaviour and the desired behaviour. The model checker used is the simulation-based Monte Carlo Model Checker for Probabilistic Linear-time Temporal Logic with numerical constraints, MC2(PLTLc). Numerical constraints as well as the overall probability of the behaviour expressed in temporal logic are used to minimise the behavioural distance. We define the theory underlying our parameter estimation approach in both the stochastic and continuous worlds. We apply our approach to biochemical systems and present an illustrative example where we estimate the kinetic rate constants in a continuous model of a signalling pathway

Steady-state conduction in self-similar billiards

The self-similar Lorentz billiard channel is a spatially extended deterministic dynamical system which consists of an infinite one-dimensional sequence of cells whose sizes increase monotonically according to their indices. This special geometry induces a nonequilibrium stationary state with particles flowing steadily from the small to the large scales. The corresponding invariant measure has fractal properties reflected by the phase-space contraction rate of the dynamics restricted to a single cell with appropriate boundary conditions. In the near-equilibrium limit, we find numerical agreement between this quantity and the entropy production rate as specified by thermodynamics