169 research outputs found
A methodology for determining amino-acid substitution matrices from set covers
We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional forms indicating how to obtain edge weights from the set
cover and, after that, substitution-matrix elements from weighted distances on
the graph, the resulting substitution matrix can be checked for performance
against some known set of reference alignments and for given gap costs. Finding
the appropriate functional forms and gap costs can then be formulated as an
optimization problem that seeks to maximize the performance of the substitution
matrix on the reference alignment set. We give computational results on the
BAliBASE suite using a genetic algorithm for optimization. Our results indicate
that it is possible to obtain substitution matrices whose performance is either
comparable to or surpasses that of several others, depending on the particular
scenario under consideration
Modeling of complex oxide materials from the first principles: systematic applications to vanadates RVO3 with distorted perovskite structure
"Realistic modeling" is a new direction of electronic structure calculations,
where the main emphasis is made on the construction of some effective
low-energy model entirely within a first-principle framework. Ideally, it is a
model in form, but with all the parameters derived rigorously, on the basis of
first-principles electronic structure calculations. The method is especially
suit for transition-metal oxides and other strongly correlated systems, whose
electronic and magnetic properties are predetermined by the behavior of some
limited number of states located near the Fermi level. After reviewing general
ideas of realistic modeling, we will illustrate abilities of this approach on
the wide series of vanadates RVO3 (R= La, Ce, Pr, Nd, Sm, Gd, Tb, Yb, and Y)
with distorted perovskite structure. Particular attention will be paid to
computational tools, which can be used for microscopic analysis of different
spin and orbital states in the partially filled t2g-band. We will explicitly
show how the lifting of the orbital degeneracy by the monoclinic distortion
stabilizes C-type antiferromagnetic (AFM) state, which can be further
transformed to the G-type AFM state by changing the crystal distortion from
monoclinic to orthorhombic one. Two microscopic mechanisms of such a
stabilization, associated with the one-electron crystal field and electron
correlation interactions, are discussed. The flexibility of the orbital degrees
of freedom is analyzed in terms of the magnetic-state dependence of interatomic
magnetic interactions.Comment: 23 pages, 13 figure
(Sub)mm Interferometry Applications in Star Formation Research
This contribution gives an overview about various applications of (sub)mm
interferometry in star formation research. The topics covered are molecular
outflows, accretion disks, fragmentation and chemical properties of low- and
high-mass star-forming regions. A short outlook on the capabilities of ALMA is
given as well.Comment: 20 pages, 7 figures, in proceedings to "2nd European School on Jets
from Young Star: High Angular Resolution Observations". A high-resolution
version of the paper can be found at
http://www.mpia.de/homes/beuther/papers.htm
Design and construction of the MicroBooNE detector
This paper describes the design and construction of the MicroBooNE liquid
argon time projection chamber and associated systems. MicroBooNE is the first
phase of the Short Baseline Neutrino program, located at Fermilab, and will
utilize the capabilities of liquid argon detectors to examine a rich assortment
of physics topics. In this document details of design specifications, assembly
procedures, and acceptance tests are reported
Measurement of prompt hadron production ratios in collisions at 0.9 and 7 TeV
The charged-particle production ratios , , ,
, and are measured with the LHCb detector using of collisions delivered by the LHC at TeV and
at TeV. The measurements are performed as a
function of transverse momentum and pseudorapidity . The
production ratios are compared to the predictions of several Monte Carlo
generator settings, none of which are able to describe adequately all
observables. The ratio is also considered as a function of rapidity
loss, , and is used to constrain models of
baryon transport.Comment: Incorrect entries in Table 2 corrected. No consequences for rest of
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