2,591 research outputs found
Quantification of the differences between quenched and annealed averaging for RNA secondary structures
The analytical study of disordered system is usually difficult due to the
necessity to perform a quenched average over the disorder. Thus, one may resort
to the easier annealed ensemble as an approximation to the quenched system. In
the study of RNA secondary structures, we explicitly quantify the deviation of
this approximation from the quenched ensemble by looking at the correlations
between neighboring bases. This quantified deviation then allows us to propose
a constrained annealed ensemble which predicts physical quantities much closer
to the results of the quenched ensemble without becoming technically
intractable.Comment: 9 pages, 14 figures, submitted to Phys. Rev.
An O(n^3)-Time Algorithm for Tree Edit Distance
The {\em edit distance} between two ordered trees with vertex labels is the
minimum cost of transforming one tree into the other by a sequence of
elementary operations consisting of deleting and relabeling existing nodes, as
well as inserting new nodes. In this paper, we present a worst-case
-time algorithm for this problem, improving the previous best
-time algorithm~\cite{Klein}. Our result requires a novel
adaptive strategy for deciding how a dynamic program divides into subproblems
(which is interesting in its own right), together with a deeper understanding
of the previous algorithms for the problem. We also prove the optimality of our
algorithm among the family of \emph{decomposition strategy} algorithms--which
also includes the previous fastest algorithms--by tightening the known lower
bound of ~\cite{Touzet} to , matching our
algorithm's running time. Furthermore, we obtain matching upper and lower
bounds of when the two trees have
different sizes and~, where .Comment: 10 pages, 5 figures, 5 .tex files where TED.tex is the main on
A New Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem: The approach of Polymers in a Random Media
We proposed a probabilistic algorithm to solve the Multiple Sequence
Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits
the representation of the Multiple Alignment between sequences as a
directed polymer in dimensions. Within this representation we can easily
track the evolution in the configuration space of the alignment through local
moves of low computational cost. At variance with other probabilistic
algorithms proposed to solve this problem, our approach allows for the creation
and deletion of gaps without extra computational cost. The algorithm was tested
aligning proteins from the kinases family. When D=3 the results are consistent
with those obtained using a complete algorithm. For where the complete
algorithm fails, we show that our algorithm still converges to reasonable
alignments. Moreover, we study the space of solutions obtained and show that
depending on the number of sequences aligned the solutions are organized in
different ways, suggesting a possible source of errors for progressive
algorithms.Comment: 7 pages and 11 figure
Thermodynamics of protein folding: a random matrix formulation
The process of protein folding from an unfolded state to a biologically
active, folded conformation is governed by many parameters e.g the sequence of
amino acids, intermolecular interactions, the solvent, temperature and chaperon
molecules. Our study, based on random matrix modeling of the interactions,
shows however that the evolution of the statistical measures e.g Gibbs free
energy, heat capacity, entropy is single parametric. The information can
explain the selection of specific folding pathways from an infinite number of
possible ways as well as other folding characteristics observed in computer
simulation studies.Comment: 21 Pages, no figure
Global unions: chasing the dream or building the reality?
This article takes as its theme the global restructuring of capital and its impact on worker organization. It argues for a reassertion of class in any analysis of global solidarity, and assesses the opportunities and barriers to effective global unionization. Rooted in the UK experience, the article analyzes the impact of the European social dimension on trade unions, before taking the discussion into a global dimension. It concludes by suggesting that there are reasons for cautious optimism in terms of solidarity building, despite difficult historical legacies and the common replacement of action with rhetoric
Counting, generating and sampling tree alignments
Pairwise ordered tree alignment are combinatorial objects that appear in RNA
secondary structure comparison. However, the usual representation of tree
alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce
identical sets of matches between identical pairs of trees. This ambiguity is
uninformative, and detrimental to any probabilistic analysis.In this work, we
consider tree alignments up to equivalence. Our first result is a precise
asymptotic enumeration of tree alignments, obtained from a context-free grammar
by mean of basic analytic combinatorics. Our second result focuses on
alignments between two given ordered trees and . By refining our grammar
to align specific trees, we obtain a decomposition scheme for the space of
alignments, and use it to design an efficient dynamic programming algorithm for
sampling alignments under the Gibbs-Boltzmann probability distribution. This
generalizes existing tree alignment algorithms, and opens the door for a
probabilistic analysis of the space of suboptimal RNA secondary structures
alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational
Biology - 2016, Jun 2016, Trujillo, Spain. 201
RNA secondary structure formation: a solvable model of heteropolymer folding
The statistical mechanics of heteropolymer structure formation is studied in
the context of RNA secondary structures. A designed RNA sequence biased
energetically towards a particular native structure (a hairpin) is used to
study the transition between the native and molten phase of the RNA as a
function of temperature. The transition is driven by a competition between the
energy gained from the polymer's overlap with the native structure and the
entropic gain of forming random contacts. A simplified Go-like model is
proposed and solved exactly. The predicted critical behavior is verified via
exact numerical enumeration of a large ensemble of similarly designed
sequences.Comment: 4 pages including 2 figure
Evolution Equation of Phenotype Distribution: General Formulation and Application to Error Catastrophe
An equation describing the evolution of phenotypic distribution is derived
using methods developed in statistical physics. The equation is solved by using
the singular perturbation method, and assuming that the number of bases in the
genetic sequence is large. Applying the equation to the mutation-selection
model by Eigen provides the critical mutation rate for the error catastrophe.
Phenotypic fluctuation of clones (individuals sharing the same gene) is
introduced into this evolution equation. With this formalism, it is found that
the critical mutation rate is sometimes increased by the phenotypic
fluctuations, i.e., noise can enhance robustness of a fitted state to mutation.
Our formalism is systematic and general, while approximations to derive more
tractable evolution equations are also discussed.Comment: 22 pages, 2 figure
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