Stable Isotropic Cosmological Singularities in Quadratic Gravity

We show that, in quadratic lagrangian theories of gravity, isotropic cosmological singularities are stable to the presence of small scalar, vector and tensor inhomogeneities. Unlike in general relativity, a particular exact isotropic solution is shown to be the stable attractor on approach to the initial cosmological singularity. This solution is also known to act as an attractor in Bianchi universes of types I, II and IX, and the results of this paper reinforce the hypothesis that small inhomogeneous and anisotropic perturbations of this attractor form part of the general cosmological solution to the field equations of quadratic gravity. Implications for the existence of a 'gravitational entropy' are also discussed.Comment: 18 pages, no figure

On the String Consensus Problem and the Manhattan Sequence Consensus Problem

In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan distance of $x$ from each of the input sequences is minimized. For binary sequences Manhattan distance coincides with Hamming distance, hence in this case the string consensus problem (also called string center problem or closest string problem) is a special case of MSC. Our main result is a practically efficient $O(l)$-time algorithm solving MSC for $k\le 5$ sequences. Practicality of our algorithms has been verified experimentally. It improves upon the quadratic algorithm by Amir et al.\ (SPIRE 2012) for string consensus problem for $k=5$ binary strings. Similarly as in Amir's algorithm we use a column-based framework. We replace the implied general integer linear programming by its easy special cases, due to combinatorial properties of the MSC for $k\le 5$. We also show that for a general parameter $k$ any instance can be reduced in linear time to a kernel of size $k!$, so the problem is fixed-parameter tractable. Nevertheless, for $k\ge 4$ this is still too large for any naive solution to be feasible in practice.Comment: accepted to SPIRE 201

Matching Reads to Many Genomes with the r-Index

The r-index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a genome in the database or to find seeds for reads that do not. This article shows how to download and install the programs ri-buildfasta and ri-align; how to call ri-buildfasta on an FASTA file to build an r-index for that file; and how to query that index with ri-align

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the main components of the FM-index in more detail, which is a rank data structure over the Burrows-Wheeler Transform () of the string that will allow us to find the interval in the string\u2019s suffix array () containing pointers to starting positions of occurrences of a given pattern; second, a sample of the that\u2014when used with the rank data structure\u2014allows us access to the . The rank data structure can be kept small even for large genomic databases, by run-length compressing the , but until recently there was no means known to keep the sample small without greatly slowing down access to the . Now that Gagie et al. (SODA 2018) have defined an sample that takes about the same space as the run-length compressed \u2014we have the design for efficient FM-indexes of genomic databases but are faced with the problem of building them. In 2018 we showed how to build the of large genomic databases efficiently (WABI 2018) but the problem of building Gagie et al.\u2019s sample efficiently was left open. We compare our approach to state-of-the-art methods for constructing the sample, and demonstrate that it is the fastest and most space-efficient method on highly repetitive genomic databases. Lastly, we apply our method for indexing partial and whole human genomes and show that it improves over Bowtie with respect to both memory and time

Prefix-free parsing for building big BWTs

High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such indexes is a challenge. Fortunately, many of these genomic databases are highly-repetitive - a characteristic that can be exploited to ease the computation of the Burrows-Wheeler Transform (BWT), which underlies many popular indexes. In this paper, we introduce a preprocessing algorithm, referred to as prefix-free parsing, that takes a text T as input, and in one-pass generates a dictionary D and a parse P of T with the property that the BWT of T can be constructed from D and P using workspace proportional to their total size and O(|T|)-time. Our experiments show that D and P are significantly smaller than T in practice, and thus, can fit in a reasonable internal memory even when T is very large. In particular, we show that with prefix-free parsing we can build an 131-MB run-length compressed FM-index (restricted to support only counting and not locating) for 1000 copies of human chromosome 19 in 2 h using 21 GB of memory, suggesting that we can build a 6.73 GB index for 1000 complete human-genome haplotypes in approximately 102 h using about 1 TB of memory

Cation distribution in manganese cobaltite spinels Co3−xMnxO4 (0 ≤ x ≤ 1) determined by thermal analysis

Thermogravimetric analysis was used in order to study the reduction in air of submicronic powders of Co3−x Mn x O4 spinels, with 0 ≤ x ≤ 1. For x = 0 (i.e. Co3O4), cation reduction occurred in a single step. It involved the CoIII ions at the octahedral sites, which were reduced to Co2+ on producing CoO. For 0 < x ≤ 1, the reduction occurred in two stages at increasing temperature with increasing amounts of manganese. The first step corresponded to the reduction of octahedral CoIII ions and the second was attributed to the reduction of octahedral Mn4+ ions to Mn3+. From the individual weight losses and the electrical neutrality of the lattice, the CoIII and Mn4+ ion concentrations were calculated. The distribution of cobalt and manganese ions present on each crystallographic site of the spinel was determined. In contrast to most previous studies that took into account either CoIII and Mn3+ or Co2+, CoIII and Mn4+ only, our thermal analysis study showed that Co2+/CoIII and Mn3+/Mn4+ pairs occupy the octahedral sites. These results were used to explain the resistivity measurements carried out on dense ceramics prepared from our powders sintered at low temperature (700–750 °C) in a Spark Plasma Sintering apparatus

Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human $\beta$-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced beta-Gaussian model to identify, with negligible computational expenditure, the most significant distortion occurring in thermal equilibrium and the associated time scales. The application of this strategy allows to gain considerable insight into the putative functional movements and, furthermore, helps to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

Soliton-Magnon Scattering in Two-Dimensional Isotropic Ferromagnets

It is studied the scattering of magnons by the 2d topological Belavin-Polyakov soliton in isotropic ferromagnet. Analytical solutions of the scattering problem are constructed: (i) exactly for any magnon wave vectors for the partial wave with the azimuthal number m=1 (translational mode), and (ii) in the long- and short-wave limits for the rest modes. The magnon mode frequencies are found for the finite size magnets. An effective equation of the soliton motion is constructed. The magnon density of states, connected with the soliton-magnon interaction, is found in a long-wave approximation.Comment: 4 pages, REVTe

Internal Modes and Magnon Scattering on Topological Solitons in 2d Easy-Axis Ferromagnets

We study the magnon modes in the presence of a topological soliton in a 2d Heisenberg easy-axis ferromagnet. The problem of magnon scattering on the soliton with arbitrary relation between the soliton radius R and the "magnetic length" Delta_0 is investigated for partial modes with different values of the azimuthal quantum numbers m. Truly local modes are shown to be present for all values of m, when the soliton radius is enough large. The eigenfrequencies of such internal modes are calculated analytically on limiting case of a large soliton radius and numerically for arbitrary soliton radius. It is demonstrated that the model of an isotropic magnet, which admits an exact analytical investigation, is not adequate even for the limit of small radius solitons, R<<Delta_0: there exists a local mode with nonzero frequency. We use the data about local modes to derive the effective equation of soliton motion; this equation has the usual Newtonian form in contrast to the case of the easy-plane ferromagnet. The effective mass of the soliton is found.Comment: 33 pages (REVTeX), 12 figures (EPS

Wetland Manipulation in the Yalahau Region of the Northern Maya Lowlands

Manipulation of wetlands for agricultural purposes by the ancient Maya of southern Mexico and Central America has been a subject of much research and debate since the 1970s. Evidence for wetland cultivation systems, in the form of drained or channelized fields, and raised planting platforms, has been restricted primarily to the southern Maya Lowlands. New research in the Yalahau region of Quintana Roo, Mexico, has recorded evidence for wetland manipulation in the far northern lowlands, in the form of rock alignments that apparently functioned to control water movement and soil accumulation in seasonally inundated areas. Nearby ancient settlements date primarily to the Late Preclassic period (ca. 100 B.C. to A.C. 350), and this age is tentatively attributed to wetland management in the area