256,359 research outputs found
Is Random Close Packing of Spheres Well Defined?
Despite its long history, there are many fundamental issues concerning random
packings of spheres that remain elusive, including a precise definition of
random close packing (RCP). We argue that the current picture of RCP cannot be
made mathematically precise and support this conclusion via a molecular
dynamics study of hard spheres using the Lubachevsky-Stillinger compression
algorithm. We suggest that this impasse can be broken by introducing the new
concept of a maximally random jammed state, which can be made precise.Comment: 6 pages total, 2 figure
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids
It has been shown that minimum free energy structure for RNAs and RNA-RNA
interaction is often incorrect due to inaccuracies in the energy parameters and
inherent limitations of the energy model. In contrast, ensemble based
quantities such as melting temperature and equilibrium concentrations can be
more reliably predicted. Even structure prediction by sampling from the
ensemble and clustering those structures by Sfold [7] has proven to be more
reliable than minimum free energy structure prediction. The main obstacle for
ensemble based approaches is the computational complexity of the partition
function and base pairing probabilities. For instance, the space complexity of
the partition function for RNA-RNA interaction is and the time
complexity is which are prohibitively large [4,12]. Our goal in this
paper is to give a fast algorithm, based on sparse folding, to calculate an
upper bound on the partition function. Our work is based on the recent
algorithm of Hazan and Jaakkola [10]. The space complexity of our algorithm is
the same as that of sparse folding algorithms, and the time complexity of our
algorithm is for single RNA and for RNA-RNA
interaction in practice, in which is the running time of sparse folding
and () is a sequence dependent parameter
Software for Exact Integration of Polynomials over Polyhedra
We are interested in the fast computation of the exact value of integrals of
polynomial functions over convex polyhedra. We present speed ups and extensions
of the algorithms presented in previous work. We present the new software
implementation and provide benchmark computations. The computation of integrals
of polynomials over polyhedral regions has many applications; here we
demonstrate our algorithmic tools solving a challenge from combinatorial voting
theory.Comment: Major updat
JGraphT -- A Java library for graph data structures and algorithms
Mathematical software and graph-theoretical algorithmic packages to
efficiently model, analyze and query graphs are crucial in an era where
large-scale spatial, societal and economic network data are abundantly
available. One such package is JGraphT, a programming library which contains
very efficient and generic graph data-structures along with a large collection
of state-of-the-art algorithms. The library is written in Java with stability,
interoperability and performance in mind. A distinctive feature of this library
is the ability to model vertices and edges as arbitrary objects, thereby
permitting natural representations of many common networks including
transportation, social and biological networks. Besides classic graph
algorithms such as shortest-paths and spanning-tree algorithms, the library
contains numerous advanced algorithms: graph and subgraph isomorphism; matching
and flow problems; approximation algorithms for NP-hard problems such as
independent set and TSP; and several more exotic algorithms such as Berge graph
detection. Due to its versatility and generic design, JGraphT is currently used
in large-scale commercial, non-commercial and academic research projects. In
this work we describe in detail the design and underlying structure of the
library, and discuss its most important features and algorithms. A
computational study is conducted to evaluate the performance of JGraphT versus
a number of similar libraries. Experiments on a large number of graphs over a
variety of popular algorithms show that JGraphT is highly competitive with
other established libraries such as NetworkX or the BGL.Comment: Major Revisio
Improved approximation of arbitrary shapes in dem simulations with multi-spheres
DEM simulations are originally made for spherical particles only. But most of real particles are anything but not spherical. Due to this problem, the multi-sphere method was invented. It provides the possibility to clump several spheres together to create complex shape structures. The proposed algorithm oļ¬ers a novel method to create multi-sphere clumps for the given arbitrary shapes. Especially the use of modern clustering algorithms, from the ļ¬eld of computational intelligence, achieve satisfactory results. The clustering is embedded into an optimisation algorithm which uses a pre-deļ¬ned criterion. A mostly unaided algorithm with only a few input and hyperparameters is able to approximate arbitrary shapes
On the enumeration of closures and environments with an application to random generation
Environments and closures are two of the main ingredients of evaluation in
lambda-calculus. A closure is a pair consisting of a lambda-term and an
environment, whereas an environment is a list of lambda-terms assigned to free
variables. In this paper we investigate some dynamic aspects of evaluation in
lambda-calculus considering the quantitative, combinatorial properties of
environments and closures. Focusing on two classes of environments and
closures, namely the so-called plain and closed ones, we consider the problem
of their asymptotic counting and effective random generation. We provide an
asymptotic approximation of the number of both plain environments and closures
of size . Using the associated generating functions, we construct effective
samplers for both classes of combinatorial structures. Finally, we discuss the
related problem of asymptotic counting and random generation of closed
environemnts and closures
A Machine-Checked Formalization of the Generic Model and the Random Oracle Model
Most approaches to the formal analyses of cryptographic protocols make the perfect cryptography assumption, i.e. the hypothese that there is no way to obtain knowledge about the plaintext pertaining to a ciphertext without knowing the key. Ideally, one would prefer to rely on a weaker hypothesis on the computational cost of gaining information about the plaintext pertaining to a ciphertext without knowing the key. Such a view is permitted by the Generic Model and the Random Oracle Model which provide non-standard computational models in which one may reason about the computational cost of breaking a cryptographic scheme. Using the proof assistant Coq, we provide a machine-checked account of the Generic Model and the Random Oracle Mode
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