Critical analysis of the Bennett-Riedel attack on secure cryptographic key distributions via the Kirchhoff-law-Johnson-noise scheme

Recently, Bennett and Riedel (BR) (http://arxiv.org/abs/1303.7435v1) argued that thermodynamics is not essential in the Kirchhoff-law–Johnson-noise (KLJN) classical physical cryptographic exchange method in an effort to disprove the security of the KLJN scheme. They attempted to demonstrate this by introducing a dissipation-free deterministic key exchange method with two batteries and two switches. In the present paper, we first show that BR's scheme is unphysical and that some elements of its assumptions violate basic protocols of secure communication. All our analyses are based on a technically unlimited Eve with infinitely accurate and fast measurements limited only by the laws of physics and statistics. For non-ideal situations and at active (invasive) attacks, the uncertainly principle between measurement duration and statistical errors makes it impossible for Eve to extract the key regardless of the accuracy or speed of her measurements. To show that thermodynamics and noise are essential for the security, we crack the BR system with 100% success via passive attacks, in ten different ways, and demonstrate that the same cracking methods do not function for the KLJN scheme that employs Johnson noise to provide security underpinned by the Second Law of Thermodynamics. We also present a critical analysis of some other claims by BR; for example, we prove that their equations for describing zero security do not apply to the KLJN scheme. Finally we give mathematical security proofs for each BR-attack against the KLJN scheme and conclude that the information theoretic (unconditional) security of the KLJN method has not been successfully challenged.Laszlo B. Kish, Derek Abbott, Claes G. Granqvis

Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes

BACKGROUND: With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows. METHODOLOGY/PRINCIPAL FINDINGS: Our algorithm, named Murasaki, makes it possible to identify anchors within multiple large sequences on the scale of several hundred megabases in few minutes using a single CPU. Two advanced features of Murasaki are (1) adaptive hash function generation, which enables efficient use of arbitrary mismatch patterns (spaced seeds) and therefore the comparison of multiple mammalian genomes in a practical amount of computation time, and (2) parallelizable execution that decreases the required wall-clock and CPU times. Murasaki can perform a sensitive anchoring of eight mammalian genomes (human, chimp, rhesus, orangutan, mouse, rat, dog, and cow) in 21 hours CPU time (42 minutes wall time). This is the first single-pass in-core anchoring of multiple mammalian genomes. We evaluated Murasaki by comparing it with the genome alignment programs BLASTZ and TBA. We show that Murasaki can anchor multiple genomes in near linear time, compared to the quadratic time requirements of BLASTZ and TBA, while improving overall accuracy. CONCLUSIONS/SIGNIFICANCE: Murasaki provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency significantly greater than existing methods. Murasaki is available under GPL at http://murasaki.sourceforge.net