Symmetry properties of the Novelli-Pak-Stoyanovskii algorithm

The number of standard Young tableaux of a fixed shape is famously given by the hook-length formula due to Frame, Robinson and Thrall. A bijective proof of Novelli, Pak and Stoyanovskii relies on a sorting algorithm akin to jeu-de-taquin which transforms an arbitrary filling of a partition into a standard Young tableau by exchanging adjacent entries. Recently, Krattenthaler and M\"uller defined the complexity of this algorithm as the average number of performed exchanges, and Neumann and the author proved it fulfils some nice symmetry properties. In this paper we recall and extend the previous results and provide new bijective proofs.Comment: 13 pages, 3 figure, submitted to FPSAC 2014 Chicag

Parallel Performance of MPI Sorting Algorithms on Dual-Core Processor Windows-Based Systems

Message Passing Interface (MPI) is widely used to implement parallel programs. Although Windowsbased architectures provide the facilities of parallel execution and multi-threading, little attention has been focused on using MPI on these platforms. In this paper we use the dual core Window-based platform to study the effect of parallel processes number and also the number of cores on the performance of three MPI parallel implementations for some sorting algorithms

Cooperative protein transport in cellular organelles

Compartmentalization into biochemically distinct organelles constantly exchanging material is one of the hallmarks of eukaryotic cells. In the most naive picture of inter-organelle transport driven by concentration gradients, concentration differences between organelles should relax. We determine the conditions under which cooperative transport, i.e. based on molecular recognition, allows for the existence and maintenance of distinct organelle identities. Cooperative transport is also shown to control the flux of material transiting through a compartmentalized system, dramatically increasing the transit time under high incoming flux. By including chemical processing of the transported species, we show that this property provides a strong functional advantage to a system responsible for protein maturation and sorting.Comment: 9 pages, 5 figure

Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatial-decomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.Comment: 33 pages, 19 figures, add references and figures are revise

Idempotent permutations

Together with a characteristic function, idempotent permutations uniquely determine idempotent maps, as well as their linearly ordered arrangement simultaneously. Furthermore, in-place linear time transformations are possible between them. Hence, they may be important for succinct data structures, information storing, sorting and searching. In this study, their combinatorial interpretation is given and their application on sorting is examined. Given an array of n integer keys each in [1,n], if it is allowed to modify the keys in the range [-n,n], idempotent permutations make it possible to obtain linearly ordered arrangement of the keys in O(n) time using only 4log(n) bits, setting the theoretical lower bound of time and space complexity of sorting. If it is not allowed to modify the keys out of the range [1,n], then n+4log(n) bits are required where n of them is used to tag some of the keys.Comment: 32 page

The Quest for Optimal Sorting Networks: Efficient Generation of Two-Layer Prefixes

Previous work identifying depth-optimal $n$-channel sorting networks for $9\leq n \leq 16$ is based on exploiting symmetries of the first two layers. However, the naive generate-and-test approach typically applied does not scale. This paper revisits the problem of generating two-layer prefixes modulo symmetries. An improved notion of symmetry is provided and a novel technique based on regular languages and graph isomorphism is shown to generate the set of non-symmetric representations. An empirical evaluation demonstrates that the new method outperforms the generate-and-test approach by orders of magnitude and easily scales until $n=40$