1,720,993 research outputs found
Real symmetric random matrices and replicas
No full textVarious ensembles of random matrices with independent entries
are analyzed by the replica formalism in the large-N limit. A result on
the Laplacian random matrix with Wigner-rescaling is generalized to
arbitrary probability distribution
MISTRAL: a tool for energy-based multiple structural alignment of proteins
No full textMotivation: The steady growth of the number of available protein structures has constantly motivated the development of new algorithms for detecting structural correspondences in proteins. Detecting structural equivalences in two or more proteins is computationally demanding as it typically entails the exploration of the combinatorial space of all possible amino acid pairings in the parent protein. The search is often aided by the introduction of various constraints such as considering protein fragments, rather than single amino acids, and/or seeking only sequential correspondences in the given proteins. An additional challenge is represented by the difficulty of associating to a given alignment, a reliable a priori measure of its statistical significance.
Results: Here we present and discuss MISTRAL, a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules. The energy minimization avoids combinatorial searches a nd returns pairwise alignment scores for which a reliable a priori statistical significance can be given.
Availability: MISTRAL is freely available for academic users as a standalone program and as a web service at http://ipht.cea.fr/protein.php
Anharmonicity and self-similarity of the free energy landscape of protein G
No full textThe near-native free-energy landscape of protein G is investigated through 0.4 s-long atomistic molecular dynamics simulations in an explicit solvent. A theoretical and computational framework is used to assess the time dependence of salient thermodynamical features. While the quasiharmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free-energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them
Simulating stochastic dynamics using large time steps
Full text linkWe present an approach to investigate the long-time stochastic dynamics of multidimensional classical systems, in contact with a heat bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short- and long-time scales and both molecular dynamics or Monte Carlo (MC) simulations are generally inefficient. Using a field theoretic approach, we perform analytically the average over the short-time stochastic fluctuations. This way, we obtain an effective theory, which generates the same long-time dynamics of the original theory, but has a lower time-resolution power. Such an approach is used to develop an improved version of the MC algorithm, which is particularly suitable to investigate the dynamics of rare conformational transitions. In the specific case of molecular systems at room temperature, we show that elementary integration time steps used to simulate the effective theory can be chosen a factor approximately 100 larger than those used in the original theory. Our results are illustrated and tested on a simple system, characterized by a rugged energy landscape
Knotted vs. unknotted proteins: evidence of knot-promoting loops.
Full text linkKnotted proteins, because of their ability to fold reversibly in the same topologically entangled conformation, are the object of an increasing number of experimental and theoretical studies. The aim of the present investigation is to assess, on the basis of presently available structural data, the extent to which knotted proteins are isolated instances in sequence or structure space, and to use comparative schemes to understand whether specific protein segments can be associated to the occurrence of a knot in the native state. A significant sequence homology is found among a sizeable group of knotted and unknotted proteins. In this family, knotted members occupy a primary sub-branch of the phylogenetic tree and differ from unknotted ones only by additional loop segments. These "knot-promoting" loops, whose virtual bridging eliminates the knot, are found in various types of knotted proteins. Valuable insight into how knots form, or are encoded, in proteins could be obtained by targeting these regions in future computational studies or excision experiments
Overlap properties and adsorption transition of two Hamiltonian paths
No full textWe consider a model of two (fully) compact polymer chains, coupled through
an attractive interaction. These compact chains are represented
by Hamiltonian paths (HP), and the coupling favors the existence of common
bonds between the chains. We use a (n=0 component) spin representation for
these paths, and we evaluate the resulting partition function within
a homogeneous saddle point approximation.
For strong coupling (i.e. at low temperature), one finds a phase
transition towards a "frozen" phase where one chain is completely
adsorbed onto the other. By performing a Legendre transform,
we obtain the probability distribution of overlaps. The fraction of
common bonds between two HP, i.e. their overlap q, has both lower
(qm) and upper (qM) bounds. This means in particular that two HP
with overlap greater than qM coincide. These results may be of
interest in (bio)polymers and in optimization problems
Phase diagram of magnetic polymers
No full textWe consider polymers made of magnetic monomers (Ising or Heisenberg-like) in a good solvent. These polymers are modeled as self-avoiding walks on a cubic lattice, and the ferromagnetic interaction between the spins carried by the monomers is short-ranged in space. At low temperature, these polymers undergo a magnetic induced first order collapse transition, that we study at the mean field level. Contrasting with an ordinary Theta point, there is a strong jump in the polymer density, as well as in its magnetization. In thr presence of a magnetic field, the collapse temperature increases: while the discontinuities decrease. Beyond a multicritical point, the transition becomes second order and Theta-like. Monte Carlo simulations for the Ising case are in qualitative agreement with these results
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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