User profiles for E. Aurell
Erik AurellProfessor 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
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 …
(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
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-…
freedom and a wide spectrum of temporal scales. In particular, we study the case of three-…
Recycling of strange sets: I. Cycle expansions
… 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 …
following sense: the value of TcIe2 ,,,E. should depend strongly on the head of the symbol …
Quasi-potential landscape in complex multi-stable systems
… 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.) …
in the electronic … (More details are included in the electronic supplementary material.) …
Optimal protocols and optimal transport in stochastic thermodynamics
… 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 …
and variance of a finite sampling will depend upon the details of the drift. It therefore makes …
Recycling of strange sets: II. Applications
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-…
low-dimensional dynamically generated strange sets: the skew Ulam map, the period-…
The inviscid Burgers equation with initial data of Brownian type
… 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…
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 …
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 …
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 …
stochastic processes describing mesoscopic systems driven by conservative or non-conservative …