398 research outputs found
Dynamical replica theoretic analysis of CDMA detection dynamics
We investigate the detection dynamics of the Gibbs sampler for code-division
multiple access (CDMA) multiuser detection. Our approach is based upon
dynamical replica theory which allows an analytic approximation to the
dynamics. We use this tool to investigate the basins of attraction when phase
coexistence occurs and examine its efficacy via comparison with Monte Carlo
simulations.Comment: 18 pages, 2 figure
Relaxation and Metastability in the RandomWalkSAT search procedure
An analysis of the average properties of a local search resolution procedure
for the satisfaction of random Boolean constraints is presented. Depending on
the ratio alpha of constraints per variable, resolution takes a time T_res
growing linearly (T_res \sim tau(alpha) N, alpha < alpha_d) or exponentially
(T_res \sim exp(N zeta(alpha)), alpha > alpha_d) with the size N of the
instance. The relaxation time tau(alpha) in the linear phase is calculated
through a systematic expansion scheme based on a quantum formulation of the
evolution operator. For alpha > alpha_d, the system is trapped in some
metastable state, and resolution occurs from escape from this state through
crossing of a large barrier. An annealed calculation of the height zeta(alpha)
of this barrier is proposed. The polynomial/exponentiel cross-over alpha_d is
not related to the onset of clustering among solutions.Comment: 23 pages, 11 figures. A mistake in sec. IV.B has been correcte
Chaos in neural networks with a nonmonotonic transfer function
Time evolution of diluted neural networks with a nonmonotonic transfer
function is analitically described by flow equations for macroscopic variables.
The macroscopic dynamics shows a rich variety of behaviours: fixed-point,
periodicity and chaos. We examine in detail the structure of the strange
attractor and in particular we study the main features of the stable and
unstable manifolds, the hyperbolicity of the attractor and the existence of
homoclinic intersections. We also discuss the problem of the robustness of the
chaos and we prove that in the present model chaotic behaviour is fragile
(chaotic regions are densely intercalated with periodicity windows), according
to a recently discussed conjecture. Finally we perform an analysis of the
microscopic behaviour and in particular we examine the occurrence of damage
spreading by studying the time evolution of two almost identical initial
configurations. We show that for any choice of the parameters the two initial
states remain microscopically distinct.Comment: 12 pages, 11 figures. Accepted for publication in Physical Review E.
Originally submitted to the neuro-sys archive which was never publicly
announced (was 9905001
Approximation schemes for the dynamics of diluted spin models: the Ising ferromagnet on a Bethe lattice
We discuss analytical approximation schemes for the dynamics of diluted spin
models. The original dynamics of the complete set of degrees of freedom is
replaced by a hierarchy of equations including an increasing number of global
observables, which can be closed approximately at different levels of the
hierarchy. We illustrate this method on the simple example of the Ising
ferromagnet on a Bethe lattice, investigating the first three possible
closures, which are all exact in the long time limit, and which yield more and
more accurate predictions for the finite-time behavior. We also investigate the
critical region around the phase transition, and the behavior of two-time
correlation functions. We finally underline the close relationship between this
approach and the dynamical replica theory under the assumption of replica
symmetry.Comment: 21 pages, 5 figure
Parmbsc1: a refined force field for DNA simulations
We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ~140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/
An initial event in insect innate immune response: structural and biological studies of interactions between β-1,3-glucan and the N-terminal domain of β-1,3-glucan recognition protein
In response to invading microorganisms, insect β-1,3-glucan recognition protein (βGRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Here we report on the NMR solution structure of the N-terminal domain of βGRP (N-βGRP) from Indian meal moth (Plodia interpunctella), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. NMR and isothermal calorimetric titrations of N-βGRP with laminarihexaose, a glucose hexamer containing β-1,3 links, suggest a weak binding of the ligand. However, addition of laminarin, a glucose polysaccharide (~ 6 kDa) containing β-1,3 and β-1,6 links that activates the proPO pathway, to N-βGRP results in the loss of NMR cross-peaks from the backbone 15N-1H groups of the protein, suggesting the formation of a large complex. Analytical ultra centrifugation (AUC) studies of formation of N-βGRP:laminarin complex show that ligand-binding induces sel-fassociation of the protein:carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (~ 102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to sub-micromolar concentrations. The structural model thus derived from the present studies for N-βGRP:laminarin complex in solution differs from the one in which a single N-βGRP molecule has been proposed to bind to a triple helical form of laminarin on the basis of an X-ray crystallographic structure of N-βGRP:laminarihexaose complex [Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., and Yamaguchi, Y. (2011) J. Biol. Chem. 286, 29158-29165]. AUC studies and phenoloxidase activation measurements carried out with the designed mutants of N-βGRP indicate that electrostatic interactions involving Asp45, Arg54, and Asp68 between the ligand-bound protein molecules contribute in part to the stability of N-βGRP:laminarin macro complex and that a decreased stability is accompanied by a reduced activation of the proPO pathway. Increased β-1,6 branching in laminarin also results in destabilization of the macro complex. These novel findings suggest that ligand-induced self-association of βGRP:β-1,3-glucan complex may form a platform on a microbial surface for recruitment of downstream proteases, as a means of amplification of the initial signal of pathogen recognition for the activation of the proPO pathway
Reliability of capturing foot parameters using digital scanning and the neutral suspension casting technique
<p>Abstract</p> <p>Background</p> <p>A clinical study was conducted to determine the intra and inter-rater reliability of digital scanning and the neutral suspension casting technique to measure six foot parameters. The neutral suspension casting technique is a commonly utilised method for obtaining a negative impression of the foot prior to orthotic fabrication. Digital scanning offers an alternative to the traditional plaster of Paris techniques.</p> <p>Methods</p> <p>Twenty one healthy participants volunteered to take part in the study. Six casts and six digital scans were obtained from each participant by two raters of differing clinical experience. The foot parameters chosen for investigation were cast length (mm), forefoot width (mm), rearfoot width (mm), medial arch height (mm), lateral arch height (mm) and forefoot to rearfoot alignment (degrees). Intraclass correlation coefficients (ICC) with 95% confidence intervals (CI) were calculated to determine the intra and inter-rater reliability. Measurement error was assessed through the calculation of the standard error of the measurement (SEM) and smallest real difference (SRD).</p> <p>Results</p> <p>ICC values for all foot parameters using digital scanning ranged between 0.81-0.99 for both intra and inter-rater reliability. For neutral suspension casting technique inter-rater reliability values ranged from 0.57-0.99 and intra-rater reliability values ranging from 0.36-0.99 for rater 1 and 0.49-0.99 for rater 2.</p> <p>Conclusions</p> <p>The findings of this study indicate that digital scanning is a reliable technique, irrespective of clinical experience, with reduced measurement variability in all foot parameters investigated when compared to neutral suspension casting.</p
IRIS Guidelines: Early Intervention in Psychosis IRIS Guidelines Update September 2012
Revision of the original 1998 IRIS Guidelines
Dynamical replica analysis of processes on finitely connected random graphs I: vertex covering
We study the stochastic dynamics of Ising spin models with random bonds,
interacting on finitely connected Poissonnian random graphs. We use the
dynamical replica method to derive closed dynamical equations for the joint
spin-field probability distribution, and solve these within the replica
symmetry ansatz. Although the theory is developed in a general setting, with a
view to future applications in various other fields, in this paper we apply it
mainly to the dynamics of the Glauber algorithm (extended with cooling
schedules) when running on the so-called vertex cover optimization problem. Our
theoretical predictions are tested against both Monte Carlo simulations and
known results from equilibrium studies. In contrast to previous dynamical
analyses based on deriving closed equations for only a small numbers of scalar
order parameters, the agreement between theory and experiment in the present
study is nearly perfect.Comment: 26 pages LaTeX, 5 figure
- …