28,473 research outputs found
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 āacceptableā. 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
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