3,095 research outputs found
High-precision covariant one-boson-exchange potentials for np scattering below 350 MeV
All realistic potential models for the two-nucleon interaction are to some
extent based on boson exchange. However, in order to achieve an essentially
perfect fit to the scattering data, characterized by a chi2/Ndata ~ 1, previous
potentials have abandoned a pure one boson-exchange mechanism (OBE). Using a
covariant theory, we have found a OBE potential that fits the 2006 world np
data below 350 MeV with a chi2/Ndata = 1.06 for 3788 data. Our potential has
fewer adjustable parameters than previous high-precision potentials, and also
reproduces the experimental triton binding energy without introducing
additional irreducible three-nucleon forces.Comment: 4 pages; revised version with augmented data sets; agrees with
published versio
Error Propagation in the Hypercycle
We study analytically the steady-state regime of a network of n error-prone
self-replicating templates forming an asymmetric hypercycle and its error tail.
We show that the existence of a master template with a higher non-catalyzed
self-replicative productivity, a, than the error tail ensures the stability of
chains in which m<n-1 templates coexist with the master species. The stability
of these chains against the error tail is guaranteed for catalytic coupling
strengths (K) of order of a. We find that the hypercycle becomes more stable
than the chains only for K of order of a2. Furthermore, we show that the
minimal replication accuracy per template needed to maintain the hypercycle,
the so-called error threshold, vanishes like sqrt(n/K) for large K and n<=4
Metastable States in High Order Short-Range Spin Glasses
The mean number of metastable states in higher order short-range spin
glasses is estimated analytically using a variational method introduced by
Tanaka and Edwards for very large coordination numbers. For lattices with small
connectivities, numerical simulations do not show any significant dependence on
the relative positions of the interacting spins on the lattice, indicating thus
that these systems can be described by a few macroscopic parameters. As an
extremely anisotropic model we consider the low autocorrelated binary spin
model and we show through numerical simulations that its landscape has an
exceptionally large number of local optima
Oriented components and their separations
[EN] There is a tight connection between connectedness, connected components, and certain types of separation spaces. Recently, axiom systems for oriented connectedness were proposed leading to the notion of reaches. Here, we introduce production relations as a further generalization of connectivity spaces and reaches and derive associated systems of oriented components that generalize connected components in a natural manner. The main result is a characterization of generalized reaches in terms of equivalent separation spaces.Stadler, BMR.; Stadler, PF. (2017). Oriented components and their separations. Applied General Topology. 18(2):255-275. doi:10.4995/agt.2017.5868SWORD25527518
Landscapes and Effective Fitness
The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged as useful conceptual tools with which to understand the dynamics of evolutionary processes, especially in the presence of complex genotype-phenotype relations. In this contribution we attempt to provide a unified discussion of these two approaches, discussing both their advantages and disadvantages in the context of some simple models. We also discuss how fitness and effective fitness change under various transformations of the configuration space of the underlying genetic model, concentrating on coarse-graining transformations and on a particular coordinate transformation that provides an appropriate basis for illuminating the structure and consequences of recombination
Multiple sequence alignments of partially coding nucleic acid sequences
BACKGROUND: High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes. RESULTS: The standard scoring scheme for nucleic acid alignments can be extended to incorporate simultaneously information on translation products in one or more reading frames. Here we present a multiple alignment tool, codaln, that implements a combined nucleic acid plus amino acid scoring model for pairwise and progressive multiple alignments that allows arbitrary weighting for almost all scoring parameters. Resource requirements of codaln are comparable with those of standard tools such as ClustalW. CONCLUSION: We demonstrate the applicability of codaln to various biologically relevant types of sequences (bacteriophage Levivirus and Vertebrate Hox clusters) and show that the combination of nucleic acid and amino acid sequence information leads to improved alignments. These, in turn, increase the performance of analysis tools that depend strictly on good input alignments such as methods for detecting conserved RNA secondary structure elements
Space shuttle food system summary, 1981-1986
All food in the Space Shuttle food system was precooked and processed so it required no refrigeration and was either ready-to-eat or could be prepared for consumption by simply adding water and/or heating. A gun-type water dispenser and a portable, suitcase-type heater were used to support this food system during the first four missions. On STS-5, new rehydratable packages were introduced along with a needle-injection water dispenser that measured the water as it was dispensed into the packages. A modular galley was developed to facilitate the meal preparation process aboard the Space Shuttle. The galley initially flew on STS-9. A personal hygiene station, a hot or cold water dispenser, a convection oven, and meal assembly areas were included in the galley
The Footprint Sorting Problem
Phylogenetic footprints are short pieces of noncoding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints in their order along the genomes. It is complicated by the fact that not all footprints are collinear: they may cross each other. The problem thus becomes the identification of the crossing footprints, the sorting of the remaining collinear cliques, and finally the insertion of the noncollinear ones at “reasonable” positions. We show that solving the footprint sorting problem requires the solution of the “Minimum Weight Vertex Feedback Set Problem”, which is known to be NP-complete and APX-hard. Nevertheless good approximations can be obtained for data sets of interest. The remaining steps of the sorting process are straightforward: computation of the transitive closure of an acyclic graph, linear extension of the resulting partial order, and finally sorting w.r.t. the linear extension. Alternatively, the footprint sorting problem can be rephrased as a combinatorial optimization problem for which approximate solutions can be obtained by means of general purpose heuristics. Footprint sortings obtained with different methods can be compared using a version of multiple sequence alignment that allows the identification of unambiguously ordered sublists. As an application we show that the rat has a slighly increased insertion/deletion rate in comparison to the mouse genome
Covariant equations for the three-body bound state
The covariant spectator (or Gross) equations for the bound state of three
identical spin 1/2 particles, in which two of the three interacting particles
are always on shell, are developed and reduced to a form suitable for numerical
solution. The equations are first written in operator form and compared to the
Bethe-Salpeter equation, then expanded into plane wave momentum states, and
finally expanded into partial waves using the three-body helicity formalism
first introduced by Wick. In order to solve the equations, the two-body
scattering amplitudes must be boosted from the overall three-body rest frame to
their individual two-body rest frames, and all effects which arise from these
boosts, including the Wigner rotations and rho-spin decomposition of the
off-shell particle, are treated exactly. In their final form, the equations
reduce to a coupled set of Faddeev-like double integral equations with
additional channels arising from the negative rho-spin states of the off-shell
particle.Comment: 57 pages, RevTeX, 6 figures, uses epsf.st
Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees
Binary relations derived from labeled rooted trees play an import role in
mathematical biology as formal models of evolutionary relationships. The
(symmetrized) Fitch relation formalizes xenology as the pairs of genes
separated by at least one horizontal transfer event. As a natural
generalization, we consider symmetrized Fitch maps, that is, symmetric maps
that assign a subset of colors to each pair of vertices in
and that can be explained by a tree with edges that are labeled with
subsets of colors in the sense that the color appears in
if and only if appears in a label along the unique path between and
in . We first give an alternative characterization of the monochromatic case
and then give a characterization of symmetrized Fitch maps in terms of
compatibility of a certain set of quartets. We show that recognition of
symmetrized Fitch maps is NP-complete. In the restricted case where
the problem becomes polynomial, since such maps
coincide with class of monochromatic Fitch maps whose graph-representations
form precisely the class of complete multi-partite graphs
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