User profiles for E. Aurell

Erik Aurell

Professor of Biological Physics, KTH-Royal Institute of Technology
Verified email at kth.se
Cited by 7135

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

M Ekeberg, C Lövkvist, Y Lan, M Weigt, E Aurell - Physical Review E, 2013 - APS
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional
(3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse …

Predictability in the large: an extension of the concept of Lyapunov exponent

E Aurell, G Boffetta, A Crisanti, G Paladin… - Journal of physics A …, 1997 - iopscience.iop.org
We investigate the predictability problem in dynamical systems with many degrees of
freedom and a wide spectrum of temporal scales. In particular, we study the case of three-…

Recycling of strange sets: I. Cycle expansions

R Artuso, E Aurell, P Cvitanovic - Nonlinearity, 1990 - iopscience.iop.org
… To proceed, we require that the tree provide a hierarchical nesting of the scaling ratios in the
following sense: the value of TcIe2 ,,,E. should depend strongly on the head of the symbol …

Quasi-potential landscape in complex multi-stable systems

JX Zhou, MDS Aliyu, E Aurell… - Journal of the Royal …, 2012 - royalsocietypublishing.org
… A numerical method, the Newton–Raphson method, is used in this paper, which is described
in the electronic … (More details are included in the electronic supplementary material.) …

Optimal protocols and optimal transport in stochastic thermodynamics

E Aurell, C Mejķa-Monasterio, P Muratore-Ginanneschi - Physical review letters, 2011 - APS
… iž1 e Ā Wi Ž, with a statistical error determined by Var―e Ā W =N. Moreover, expectation
and variance of a finite sampling will depend upon the details of the drift. It therefore makes …

Recycling of strange sets: II. Applications

R Artuso, E Aurell, P Cvitanovic - Nonlinearity, 1990 - iopscience.iop.org
For pt. I see ibid., vol. 3, no. 2, p. 325-59 (1990). Cycle expansions are applied to a series of
low-dimensional dynamically generated strange sets: the skew Ulam map, the period-…

The inviscid Burgers equation with initial data of Brownian type

ZS She, E Aurell, U Frisch - Communications in mathematical physics, 1992 - Springer
… l(e), we plot also the graph of (the inverse of) a randomized version of the standard Devil's
staircase. (Randomizing means that we shift randomly the position of jumps.) Observe that Fig…

Inverse Ising inference using all the data

E Aurell, M Ekeberg - Physical review letters, 2012 - APS
We show that a method based on logistic regression, using all the data, solves the inverse
Ising problem far better than mean-field calculations relying only on sample pairwise …

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

M Ekeberg, T Hartonen, E Aurell - Journal of Computational Physics, 2014 - Elsevier
Direct-coupling analysis is a group of methods to harvest information about coevolving residues
in a protein family by learning a generative model in an exponential family from data. In …

Refined second law of thermodynamics for fast random processes

E Aurell, K Gawȩdzki, C Mejķa-Monasterio… - Journal of statistical …, 2012 - Springer
We establish a refined version of the Second Law of Thermodynamics for Langevin
stochastic processes describing mesoscopic systems driven by conservative or non-conservative …