Selecting fast folding proteins by their rate of convergence

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using only the very initial parts of the dynamical trajectories. It does not require any preliminary knowledge of the native state and can be applied to different kinds of models, including atomistic descriptions. We tested the method within both the lattice and off-lattice model frameworks and obtained several so far unknown good folders. The unbiased algorithm also allows to determine the optimal folding temperature and takes at least 3--4 orders of magnitude less time steps than those needed to compute folding times

Eigenvalue Separation in Some Random Matrix Models

The eigenvalue density for members of the Gaussian orthogonal and unitary ensembles follows the Wigner semi-circle law. If the Gaussian entries are all shifted by a constant amount c/Sqrt(2N), where N is the size of the matrix, in the large N limit a single eigenvalue will separate from the support of the Wigner semi-circle provided c > 1. In this study, using an asymptotic analysis of the secular equation for the eigenvalue condition, we compare this effect to analogous effects occurring in general variance Wishart matrices and matrices from the shifted mean chiral ensemble. We undertake an analogous comparative study of eigenvalue separation properties when the size of the matrices are fixed and c goes to infinity, and higher rank analogues of this setting. This is done using exact expressions for eigenvalue probability densities in terms of generalized hypergeometric functions, and using the interpretation of the latter as a Green function in the Dyson Brownian motion model. For the shifted mean Gaussian unitary ensemble and its analogues an alternative approach is to use exact expressions for the correlation functions in terms of classical orthogonal polynomials and associated multiple generalizations. By using these exact expressions to compute and plot the eigenvalue density, illustrations of the various eigenvalue separation effects are obtained.Comment: 25 pages, 9 figures include

Heteroclinic Chaos, Chaotic Itinerancy and Neutral Attractors in Symmetrical Replicator Equations with Mutations

A replicator equation with mutation processes is numerically studied. Without any mutations, two characteristics of the replicator dynamics are known: an exponential divergence of the dominance period, and hierarchical orderings of the attractors. A mutation introduces some new aspects: the emergence of structurally stable attractors, and chaotic itinerant behavior. In addition, it is reported that a neutral attractor can exist in the mutataion rate -> +0 region.Comment: 4 pages, 9 figure

Segregation by thermal diffusion in granular shear flows

Segregation by thermal diffusion of an intruder immersed in a sheared granular gas is analyzed from the (inelastic) Boltzmann equation. Segregation is induced by the presence of a temperature gradient orthogonal to the shear flow plane and parallel to gravity. We show that, like in analogous systems without shear, the segregation criterion yields a transition between upwards segregation and downwards segregation. The form of the phase diagrams is illustrated in detail showing that they depend sensitively on the value of gravity relative to the thermal gradient. Two specific situations are considered: i) absence of gravity, and ii) homogeneous temperature. We find that both mechanisms (upwards and downwards segregation) are stronger and more clearly separated when compared with segregation criteria in systems without shear.Comment: 8 figures. To appear in J. Stat. Mec

Rethinking the patient: using Burden of Treatment Theory to understand the changing dynamics of illness

<b>Background</b> In this article we outline Burden of Treatment Theory, a new model of the relationship between sick people, their social networks, and healthcare services. Health services face the challenge of growing populations with long-term and life-limiting conditions, they have responded to this by delegating to sick people and their networks routine work aimed at managing symptoms, and at retarding - and sometimes preventing - disease progression. This is the new proactive work of patient-hood for which patients are increasingly accountable: founded on ideas about self-care, self-empowerment, and self-actualization, and on new technologies and treatment modalities which can be shifted from the clinic into the community. These place new demands on sick people, which they may experience as burdens of treatment.<p></p> <b>Discussion</b> As the burdens accumulate some patients are overwhelmed, and the consequences are likely to be poor healthcare outcomes for individual patients, increasing strain on caregivers, and rising demand and costs of healthcare services. In the face of these challenges we need to better understand the resources that patients draw upon as they respond to the demands of both burdens of illness and burdens of treatment, and the ways that resources interact with healthcare utilization.<p></p> <b>Summary</b> Burden of Treatment Theory is oriented to understanding how capacity for action interacts with the work that stems from healthcare. Burden of Treatment Theory is a structural model that focuses on the work that patients and their networks do. It thus helps us understand variations in healthcare utilization and adherence in different healthcare settings and clinical contexts

Measurement of transparency ratios for protons from short-range correlated pairs

Nuclear transparency, Tp(A), is a measure of the average probability for a struck proton to escape the nucleus without significant re-interaction. Previously, nuclear transparencies were extructed for quasi-elastic A(e,e'p) knockout of protons with momentum below the Fermi momentum, where the spectral functions are well known. In this paper we extract a novel observable, the transparency ratio, Tp(A)/T_p(12C), for knockout of high-missing-momentum protons from the breakup of short range correlated pairs (2N-SRC) in Al, Fe and Pb nuclei relative to C. The ratios were measured at momentum transfer Q^2 > 1.5 (GeV/c)^2 and x_B > 1.2 where the reaction is expected to be dominated by electron scattering from 2N-SRC. The transparency ratios of the knocked-out protons coming from 2N-SRC breakup are 20 - 30% lower than those of previous results for low missing momentum. They agree with Glauber calculations and agree with renormalization of the previously published transparencies as proposed by recent theoretical investigations. The new transparencies scale as A^-1/3, which is consistent with dominance of scattering from nucleons at the nuclear surface.Comment: 6 pages, 4 figure

Statistics of Certain Models of Evolution

In a recent paper, Newman surveys the literature on power law spectra in evolution, self-organised criticality and presents a model of his own to arrive at a conclusion that self-organised criticality is not necessary for evolution. Not only did he miss a key model (Ecolab) that has a clear self-organised critical mechanism, but also Newman's model exhibits the same mechanism that gives rise to power law behaviour as does Ecolab. Newman's model is, in fact, a ``mean field'' approximation of a self-organised critical system. In this paper, I have also implemented Newman's model using the Ecolab software, removing the restriction that the number of species remains constant. It turns out that the requirement of constant species number is non-trivial, leading to a global coupling between species that is similar in effect to the species interactions seen in Ecolab. In fact, the model must self-organise to a state where the long time average of speciations balances that of the extinctions, otherwise the system either collapses or explodes. In view of this, Newman's model does not provide the hoped-for counter example to the presence of self-organised criticality in evolution, but does provide a simple, almost analytic model that can used to understand more intricate models such as Ecolab.Comment: accepted in Phys Rev E.; RevTeX; See http://parallel.hpc.unsw.edu.au/rks/ecolab.html for more informatio

Assessing and countering reaction attacks against post-quantum public-key cryptosystems based on QC-LDPC codes

Code-based public-key cryptosystems based on QC-LDPC and QC-MDPC codes are promising post-quantum candidates to replace quantum vulnerable classical alternatives. However, a new type of attacks based on Bob's reactions have recently been introduced and appear to significantly reduce the length of the life of any keypair used in these systems. In this paper we estimate the complexity of all known reaction attacks against QC-LDPC and QC-MDPC code-based variants of the McEliece cryptosystem. We also show how the structure of the secret key and, in particular, the secret code rate affect the complexity of these attacks. It follows from our results that QC-LDPC code-based systems can indeed withstand reaction attacks, on condition that some specific decoding algorithms are used and the secret code has a sufficiently high rate.Comment: 21 pages, 2 figures, to be presented at CANS 201