60,672 research outputs found
Algorithm engineering for optimal alignment of protein structure distance matrices
Protein structural alignment is an important problem in computational
biology. In this paper, we present first successes on provably optimal pairwise
alignment of protein inter-residue distance matrices, using the popular Dali
scoring function. We introduce the structural alignment problem formally, which
enables us to express a variety of scoring functions used in previous work as
special cases in a unified framework. Further, we propose the first
mathematical model for computing optimal structural alignments based on dense
inter-residue distance matrices. We therefore reformulate the problem as a
special graph problem and give a tight integer linear programming model. We
then present algorithm engineering techniques to handle the huge integer linear
programs of real-life distance matrix alignment problems. Applying these
techniques, we can compute provably optimal Dali alignments for the very first
time
Computational analysis of folding and mutation properties of C5 domain from Myosin binding protein C
Thermal folding Molecular Dynamics simulations of the domain C5 from Myosin
Binding Protein C were performed using a native-centric model to study the role
of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of
Asn755 causes the largest shift of the folding temperature, and the residue is
located in the CFGA' beta-sheet featuring the highest Phi-values. The mutation
thus appears to reduce the thermodynamic stability in agreement with
experimental data. The mutations on Arg654 and Arg668, conversely, cause a
little change in the folding temperature and they reside in the low Phi-value
BDE beta-sheet, so that their pathologic role cannot be related to impairment
of the folding process but possibly to the binding with target molecules. As
the typical signature of Domain C5 is the presence of a longer and
destabilizing CD-loop with respect to the other Ig-like domains we completed
the work with a bioinformatic analysis of this loop showing a high density of
negative charge and low hydrophobicity. This indicates the CD-loop as a
natively unfolded sequence with a likely coupling between folding and ligand
binding.Comment: RevTeX, 10 pages, 9 eps-figure
Topic and background knowledge effects on performance in speaking assessment
This study explores the extent to which topic and background knowledge of topic affect spoken
performance in a high-stakes speaking test. It is argued that evidence of a substantial influence may introduce construct-irrelevant variance and undermine test fairness. Data were collected from 81 non-native speakers of English who performed on 10 topics across three task types. Background knowledge and general language proficiency were measured using self-report questionnaires and C-tests respectively. Score data were analysed using many-facet Rasch measurement and multiple regression. Findings showed that for two of the three task types, the topics used in the study generally exhibited difficulty measures which were statistically distinct. However, the size of the differences in topic difficulties was too small to have a large practical effect on scores. Participants’ different levels of background knowledge were shown to have a systematic effect on performance. However, these statistically significant differences also failed to translate into practical significance. Findings hold implications for speaking performance assessment
Holographic Mutual Information for Singular Surfaces
We study corner contributions to holographic mutual information for
entangling regions composed of a set of disjoint sectors of a single infinite
circle in three-dimensional conformal field theories. In spite of the UV
divergence of holographic mutual information, it exhibits a first order phase
transition. We show that tripartite information is also divergent for disjoint
sectors, which is in contrast with the well-known feature of tripartite
information being finite even when entangling regions share boundaries. We also
verify the locality of corner effects by studying mutual information between
regions separated by a sharp annular region. Possible extensions to higher
dimensions and hyperscaling violating geometries is also considered for
disjoint sectors.Comment: 35 pages, 25 Figures, v2: presentation improved, v3: matches
published version in JHE
Density bounds for outer parallel domains of unit ball packings
We give upper bounds for the density of unit ball packings relative to their
outer parallel domains and discuss their connection to contact numbers. Also,
packings of soft balls are introduced and upper bounds are given for the
fraction of space covered by them.Comment: 22 pages, 1 figur
The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits
PMCID: PMC3410907This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The ice-limit of Coulomb gauge Yang-Mills theory
In this paper we describe gauge invariant multi-quark states generalising the
path integral framework developed by Parrinello, Jona-Lasinio and Zwanziger to
amend the Faddeev-Popov approach. This allows us to produce states such that,
in a limit which we call the ice-limit, fermions are dressed with glue
exclusively from the fundamental modular region associated with Coulomb gauge.
The limit can be taken analytically without difficulties, avoiding the Gribov
problem. This is llustrated by an unambiguous construction of gauge invariant
mesonic states for which we simulate the static quark--antiquark potential.Comment: 25 pages, 4 figure
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