2,188 research outputs found
Dynamical study of the hyperextended scalar-tensor theory in the empty Bianchi type I model
The dynamics of the hyperextended scalar-tensor theory in the empty Bianchi
type I model is investigated. We describe a method giving the sign of the first
and second derivatives of the metric functions whatever the coupling function.
Hence, we can predict if a theory gives birth to expanding, contracting,
bouncing or inflationary cosmology. The dynamics of a string inspired theory
without antisymetric field strength is analysed. Some exact solutions are
found.Comment: 18 pages, 3 figure
The phase space view of f(R) gravity
We study the geometry of the phase space of spatially flat
Friedmann-Lemaitre-Robertson-Walker models in f(R) gravity, for a general form
of the function f(R). The equilibrium points (de Sitter spaces) and their
stability are discussed, and a comparison is made with the phase space of the
equivalent scalar-tensor theory. New effective Lagrangians and Hamiltonians are
also presented.Comment: 14 pages, 2 figures, published in Classical and Quantum Gravity;
references adde
f(R) theories
Over the past decade, f(R) theories have been extensively studied as one of
the simplest modifications to General Relativity. In this article we review
various applications of f(R) theories to cosmology and gravity - such as
inflation, dark energy, local gravity constraints, cosmological perturbations,
and spherically symmetric solutions in weak and strong gravitational
backgrounds. We present a number of ways to distinguish those theories from
General Relativity observationally and experimentally. We also discuss the
extension to other modified gravity theories such as Brans-Dicke theory and
Gauss-Bonnet gravity, and address models that can satisfy both cosmological and
local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in
Relativity, Published version, Comments are welcom
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
RosettaDock has been increasingly used in protein docking and design strategies in order to predict the structure of protein-protein interfaces. Here we test capabilities of RosettaDock 3.2, part of the newly developed Rosetta v3.2 modeling suite, against Docking Benchmark 3.0, and compare it with RosettaDock v2.3, the latest version of the previous Rosetta software package. The benchmark contains a diverse set of 116 docking targets including 22 antibody-antigen complexes, 33 enzyme-inhibitor complexes, and 60 ‘other’ complexes. These targets were further classified by expected docking difficulty into 84 rigid-body targets, 17 medium targets, and 14 difficult targets. We carried out local docking perturbations for each target, using the unbound structures when available, in both RosettaDock v2.3 and v3.2. Overall the performances of RosettaDock v2.3 and v3.2 were similar. RosettaDock v3.2 achieved 56 docking funnels, compared to 49 in v2.3. A breakdown of docking performance by protein complex type shows that RosettaDock v3.2 achieved docking funnels for 63% of antibody-antigen targets, 62% of enzyme-inhibitor targets, and 35% of ‘other’ targets. In terms of docking difficulty, RosettaDock v3.2 achieved funnels for 58% of rigid-body targets, 30% of medium targets, and 14% of difficult targets. For targets that failed, we carry out additional analyses to identify the cause of failure, which showed that binding-induced backbone conformation changes account for a majority of failures. We also present a bootstrap statistical analysis that quantifies the reliability of the stochastic docking results. Finally, we demonstrate the additional functionality available in RosettaDock v3.2 by incorporating small-molecules and non-protein co-factors in docking of a smaller target set. This study marks the most extensive benchmarking of the RosettaDock module to date and establishes a baseline for future research in protein interface modeling and structure prediction
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