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

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

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 $O(n^4)$ and the time complexity is $O(n^6)$ 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 $O(MFE(n)\ell)$ for single RNA and $O(MFE(m, n)\ell)$ for RNA-RNA interaction in practice, in which $MFE$ is the running time of sparse folding and $\ell \leq n$ ($\ell \leq n + m$) is a sequence dependent parameter

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

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

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 offers a novel method to create multi-sphere clumps for the given arbitrary shapes. Especially the use of modern clustering algorithms, from the field of computational intelligence, achieve satisfactory results. The clustering is embedded into an optimisation algorithm which uses a pre-defined criterion. A mostly unaided algorithm with only a few input and hyperparameters is able to approximate arbitrary shapes