2,984 research outputs found
Development of the Trident 1 aerodynamic saike mechanism
The Aerospike drag reduction mechanism was designed and developed for use on the Trident I submarine launched ballistic missile. This mechanism encounters a unique combination of environments necessitating unique design solutions to ensure satisfactory operation over its design life. The development of the Aerospike is reviewed emphasizing the unique and interesting problems encountered and their solutions
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
Exact Asymptotic Results for a Model of Sequence Alignment
Finding analytically the statistics of the longest common subsequence (LCS)
of a pair of random sequences drawn from c alphabets is a challenging problem
in computational evolutionary biology. We present exact asymptotic results for
the distribution of the LCS in a simpler, yet nontrivial, variant of the
original model called the Bernoulli matching (BM) model which reduces to the
original model in the large c limit. We show that in the BM model, for all c,
the distribution of the asymptotic length of the LCS, suitably scaled, is
identical to the Tracy-Widom distribution of the largest eigenvalue of a random
matrix whose entries are drawn from a Gaussian unitary ensemble. In particular,
in the large c limit, this provides an exact expression for the asymptotic
length distribution in the original LCS problem.Comment: 4 pages Revtex, 2 .eps figures include
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
funcX: A Federated Function Serving Fabric for Science
Exploding data volumes and velocities, new computational methods and
platforms, and ubiquitous connectivity demand new approaches to computation in
the sciences. These new approaches must enable computation to be mobile, so
that, for example, it can occur near data, be triggered by events (e.g.,
arrival of new data), be offloaded to specialized accelerators, or run remotely
where resources are available. They also require new design approaches in which
monolithic applications can be decomposed into smaller components, that may in
turn be executed separately and on the most suitable resources. To address
these needs we present funcX---a distributed function as a service (FaaS)
platform that enables flexible, scalable, and high performance remote function
execution. funcX's endpoint software can transform existing clouds, clusters,
and supercomputers into function serving systems, while funcX's cloud-hosted
service provides transparent, secure, and reliable function execution across a
federated ecosystem of endpoints. We motivate the need for funcX with several
scientific case studies, present our prototype design and implementation, show
optimizations that deliver throughput in excess of 1 million functions per
second, and demonstrate, via experiments on two supercomputers, that funcX can
scale to more than more than 130000 concurrent workers.Comment: Accepted to ACM Symposium on High-Performance Parallel and
Distributed Computing (HPDC 2020). arXiv admin note: substantial text overlap
with arXiv:1908.0490
Exact solution of the Bernoulli matching model of sequence alignment
Through a series of exact mappings we reinterpret the Bernoulli model of
sequence alignment in terms of the discrete-time totally asymmetric exclusion
process with backward sequential update and step function initial condition.
Using earlier results from the Bethe ansatz we obtain analytically the exact
distribution of the length of the longest common subsequence of two sequences
of finite lengths . Asymptotic analysis adapted from random matrix theory
allows us to derive the thermodynamic limit directly from the finite-size
result.Comment: 13 pages, 4 figure
Bethe Ansatz in the Bernoulli Matching Model of Random Sequence Alignment
For the Bernoulli Matching model of sequence alignment problem we apply the
Bethe ansatz technique via an exact mapping to the 5--vertex model on a square
lattice. Considering the terrace--like representation of the sequence alignment
problem, we reproduce by the Bethe ansatz the results for the averaged length
of the Longest Common Subsequence in Bernoulli approximation. In addition, we
compute the average number of nucleation centers of the terraces.Comment: 14 pages, 5 figures (some points are clarified
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
Addition-Deletion Networks
We study structural properties of growing networks where both addition and
deletion of nodes are possible. Our model network evolves via two independent
processes. With rate r, a node is added to the system and this node links to a
randomly selected existing node. With rate 1, a randomly selected node is
deleted, and its parent node inherits the links of its immediate descendants.
We show that the in-component size distribution decays algebraically, c_k ~
k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with
the addition rate r. Structural properties of the network including the height
distribution, the diameter of the network, the average distance between two
nodes, and the fraction of dangling nodes are also obtained analytically.
Interestingly, the deletion process leads to a giant hub, a single node with a
macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure
Parental bonding and identity style as correlates of self-esteem among adult adoptees and nonadoptees
Adult adoptees (n equals 100) and non-adoptees (n equals 100) were compared with regard to selfesteem, identity processing style, and parental bonding. While some differences were found with regard to self-esteem, maternal care, and maternal overprotection, these differences were
qualified by reunion status such that only reunited adoptees differed significantly from nonadoptees.
Moreover, hierarchical regression analyses indicated that parental bonding and identity processing style were more important than adoptive status per se in predicting self esteem. Implications for practitioners who work with adoptees are discussed
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