124,337 research outputs found
A Self-Organizing Algorithm for Modeling Protein Loops
Protein loops, the flexible short segments connecting two stable secondary
structural units in proteins, play a critical role in protein structure and
function. Constructing chemically sensible conformations of protein loops that
seamlessly bridge the gap between the anchor points without introducing any
steric collisions remains an open challenge. A variety of algorithms have been
developed to tackle the loop closure problem, ranging from inverse kinematics to
knowledge-based approaches that utilize pre-existing fragments extracted from
known protein structures. However, many of these approaches focus on the
generation of conformations that mainly satisfy the fixed end point condition,
leaving the steric constraints to be resolved in subsequent post-processing
steps. In the present work, we describe a simple solution that simultaneously
satisfies not only the end point and steric conditions, but also chirality and
planarity constraints. Starting from random initial atomic coordinates, each
individual conformation is generated independently by using a simple alternating
scheme of pairwise distance adjustments of randomly chosen atoms, followed by
fast geometric matching of the conformationally rigid components of the
constituent amino acids. The method is conceptually simple, numerically stable
and computationally efficient. Very importantly, additional constraints, such as
those derived from NMR experiments, hydrogen bonds or salt bridges, can be
incorporated into the algorithm in a straightforward and inexpensive way, making
the method ideal for solving more complex multi-loop problems. The remarkable
performance and robustness of the algorithm are demonstrated on a set of protein
loops of length 4, 8, and 12 that have been used in previous studies
Performance and Optimization Abstractions for Large Scale Heterogeneous Systems in the Cactus/Chemora Framework
We describe a set of lower-level abstractions to improve performance on
modern large scale heterogeneous systems. These provide portable access to
system- and hardware-dependent features, automatically apply dynamic
optimizations at run time, and target stencil-based codes used in finite
differencing, finite volume, or block-structured adaptive mesh refinement
codes.
These abstractions include a novel data structure to manage refinement
information for block-structured adaptive mesh refinement, an iterator
mechanism to efficiently traverse multi-dimensional arrays in stencil-based
codes, and a portable API and implementation for explicit SIMD vectorization.
These abstractions can either be employed manually, or be targeted by
automated code generation, or be used via support libraries by compilers during
code generation. The implementations described below are available in the
Cactus framework, and are used e.g. in the Einstein Toolkit for relativistic
astrophysics simulations
Optimal Discrete Uniform Generation from Coin Flips, and Applications
This article introduces an algorithm to draw random discrete uniform
variables within a given range of size n from a source of random bits. The
algorithm aims to be simple to implement and optimal both with regards to the
amount of random bits consumed, and from a computational perspective---allowing
for faster and more efficient Monte-Carlo simulations in computational physics
and biology. I also provide a detailed analysis of the number of bits that are
spent per variate, and offer some extensions and applications, in particular to
the optimal random generation of permutations.Comment: first draft, 22 pages, 5 figures, C code implementation of algorith
Probing the Space of Toric Quiver Theories
We demonstrate a practical and efficient method for generating toric Calabi-Yau quiver theories, applicable to both D3 and M2 brane world-volume physics. A new analytic method is presented at low order parametres and an algorithm for the general case is developed which has polynomial complexity in the number of edges in the quiver. Using this algorithm, carefully implemented, we classify the quiver diagram and assign possible superpotentials for various small values of the number of edges and nodes. We examine some preliminary statistics on this space of toric quiver theories
TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots
We present TT2NE, a new algorithm to predict RNA secondary structures with
pseudoknots. The method is based on a classification of RNA structures
according to their topological genus. TT2NE guarantees to find the minimum free
energy structure irrespectively of pseudoknot topology. This unique proficiency
is obtained at the expense of the maximum length of sequence that can be
treated but comparison with state-of-the-art algorithms shows that TT2NE is a
very powerful tool within its limits. Analysis of TT2NE's wrong predictions
sheds light on the need to study how sterical constraints limit the range of
pseudoknotted structures that can be formed from a given sequence. An
implementation of TT2NE on a public server can be found at
http://ipht.cea.fr/rna/tt2ne.php
Controlled non uniform random generation of decomposable structures
Consider a class of decomposable combinatorial structures, using different
types of atoms \Atoms = \{\At_1,\ldots ,\At_{|{\Atoms}|}\}. We address the
random generation of such structures with respect to a size and a targeted
distribution in of its \emph{distinguished} atoms. We consider two
variations on this problem. In the first alternative, the targeted distribution
is given by real numbers \TargFreq_1, \ldots, \TargFreq_k such that 0 <
\TargFreq_i < 1 for all and \TargFreq_1+\cdots+\TargFreq_k \leq 1. We
aim to generate random structures among the whole set of structures of a given
size , in such a way that the {\em expected} frequency of any distinguished
atom \At_i equals \TargFreq_i. We address this problem by weighting the
atoms with a -tuple \Weights of real-valued weights, inducing a weighted
distribution over the set of structures of size . We first adapt the
classical recursive random generation scheme into an algorithm taking
\bigO{n^{1+o(1)}+mn\log{n}} arithmetic operations to draw structures from
the \Weights-weighted distribution. Secondly, we address the analytical
computation of weights such that the targeted frequencies are achieved
asymptotically, i. e. for large values of . We derive systems of functional
equations whose resolution gives an explicit relationship between \Weights
and \TargFreq_1, \ldots, \TargFreq_k. Lastly, we give an algorithm in
\bigO{k n^4} for the inverse problem, {\it i.e.} computing the frequencies
associated with a given -tuple \Weights of weights, and an optimized
version in \bigO{k n^2} in the case of context-free languages. This allows
for a heuristic resolution of the weights/frequencies relationship suitable for
complex specifications. In the second alternative, the targeted distribution is
given by a natural numbers such that
where is the number of undistinguished atoms.
The structures must be generated uniformly among the set of structures of size
that contain {\em exactly} atoms \At_i (). We give
a \bigO{r^2\prod_{i=1}^k n_i^2 +m n k \log n} algorithm for generating
structures, which simplifies into a \bigO{r\prod_{i=1}^k n_i +m n} for
regular specifications
A Simple and Scalable Static Analysis for Bound Analysis and Amortized Complexity Analysis
We present the first scalable bound analysis that achieves amortized
complexity analysis. In contrast to earlier work, our bound analysis is not
based on general purpose reasoners such as abstract interpreters, software
model checkers or computer algebra tools. Rather, we derive bounds directly
from abstract program models, which we obtain from programs by comparatively
simple invariant generation and symbolic execution techniques. As a result, we
obtain an analysis that is more predictable and more scalable than earlier
approaches. Our experiments demonstrate that our analysis is fast and at the
same time able to compute bounds for challenging loops in a large real-world
benchmark. Technically, our approach is based on lossy vector addition systems
(VASS). Our bound analysis first computes a lexicographic ranking function that
proves the termination of a VASS, and then derives a bound from this ranking
function. Our methodology achieves amortized analysis based on a new insight
how lexicographic ranking functions can be used for bound analysis
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