1,354 research outputs found
Shape of a liquid front upon dewetting
We examine the profile of a liquid front of a film that is dewetting a solid
substrate. Since volume is conserved, the material that once covered the
substrate is accumulated in a rim close to the three phase contact line.
Theoretically, such a profile of a Newtonian liquid resembles an exponentially
decaying harmonic oscillation that relaxes into the prepared film thickness.
For the first time, we were able to observe this behavior experimentally. A
non-Newtonian liquid - a polymer melt - however, behaves differently. Here,
viscoelastic properties come into play. We will demonstrate that by analyzing
the shape of the rim profile. On a nm scale, we gain access to the rheology of
a non-Newtonian liquid.Comment: 4 pages, 4 figure
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
Generalized Fitch Graphs II: Sets of Binary Relations that are explained by Edge-labeled Trees
Fitch graphs are digraphs that are explained by -edge-labeled rooted trees with leaf set : there is an arc if and only if the unique path in that connects the last common
ancestor of and with contains at least one edge
with label "1". In practice, Fitch graphs represent xenology relations, i.e.,
pairs of genes and for which a horizontal gene transfer happened along
the path from to .
In this contribution, we generalize the concept of Fitch graphs and consider
trees that are equipped with edge-labeling
that assigns to each edge a subset of colors. Given such a
tree, we can derive a map (or equivalently a set of
not necessarily disjoint binary relations), such that (or equivalently ) with , if and only if there is at least one edge with color from
to .
The central question considered here: Is a given map a Fitch
map, i.e., is there there an edge-labeled tree with
, and thus explains ?
Here, we provide a characterization of Fitch maps in terms of certain
neighborhoods and forbidden submaps. Further restrictions of Fitch maps are
considered. Moreover, we show that the least-resolved tree explaining a Fitch
map is unique (up to isomorphism). In addition, we provide a polynomial-time
algorithm to decide whether is a Fitch map and, in the
affirmative case, to construct the (up to isomorphism) unique least-resolved
tree that explains
Approaching ‘kit-type’ labelling with 68Ga: the DATA chelators
The DATA chelators are a novel class of tri-anionic ligands based on 6-amino-1,4-diazepine-triacetic acid, which have been introduced recently for the chelation of 68Ga. Compared with macrocyclic chelators based on the cyclen scaffold (i.e., DOTA, DO3A, and DO2A derivatives), DATA chelators undergo quantitative radiolabelling more rapidly and under milder conditions. In this study, a systematic evaluation of the labelling of four DATA chelators—DATAM, DATAP, DATAPh, and DATAPPh—with 68Ga is presented. The results highlight the extraordinary potential of this new class of chelators for application in molecular imaging using 68Ga positron emission tomography (PET)
Generic morphologies of viscoelastic dewetting fronts
A simple model is put forward which accounts for the occurrence of certain
generic dewetting morphologies in thin liquid coatings. It demonstrates that by
taking into account the elastic properties of the coating, a morphological
phase diagram may be derived which describes the observed structures of
dewetting fronts. It is demonstrated that dewetting morphologies may also serve
to determine nanoscale rheological properties of liquids.Comment: 4 pages, 2 figure
Thickness-dependent spontaneous dewetting morphology of ultrathin Ag films
We show here that the morphological pathway of spontaneous dewetting of
ultrathin Ag films on SiO2 under nanosecond laser melting is found to be film
thickness dependent. For films with thickness h between 2 <= h <= 9.5 nm, the
morphology during the intermediate stages of dewetting consisted of
bicontinuous structures. For films 11.5 <= h <= 20 nm, the intermediate stages
consisted of regularly-sized holes. Measurement of the characteristic length
scales for different stages of dewetting as a function of film thickness showed
a systematic increase, which is consistent with the spinodal dewetting
instability over the entire thickness range investigated. This change in
morphology with thickness is consistent with observations made previously for
polymer films [A. Sharma et al, Phys. Rev. Lett., v81, pp3463 (1998); R.
Seemann et al, J. Phys. Cond. Matt., v13, pp4925, (2001)]. Based on the
behavior of free energy curvature that incorporates intermolecular forces, we
have estimated the morphological transition thickness for the intermolecular
forces for Ag on SiO2 . The theory predictions agree well with observations for
Ag. These results show that it is possible to form a variety of complex Ag
nanomorphologies in a consistent manner, which could be useful in optical
applications of Ag surfaces, such as in surface enhanced Raman sensing.Comment: 20 pages, 5 figure
Cardiac cell modelling: Observations from the heart of the cardiac physiome project
In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field
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Detection of RNA structures in porcine EST data and related mammals
RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Non-coding RNAs (ncRNAs) are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and mRNA like ncRNAs in eukaryotes. To investigate this further, we examined the large data set in the Sino-Danish PigEST resource http://pigest.ku.dk which also contains expression information distributed on 97 non-normalized cDNA libraries. Results We constructed a pipeline, EST2ncRNA, to search for known and novel ncRNAs. The pipeline utilises sequence similarity to ncRNA databases (blast), structure similarity to Rfam (RaveNnA) as well as multiple alignments to predict conserved novel putative RNA structures (RNAz). EST2ncRNA was fed with 48,000 contigs and 73,000 singletons available from the PigEST resource. Using the pipeline we identified known RNA structures in 137 contigs and single reads (conreads), and predicted high confidence RNA structures in non-protein coding regions of additional 1,262 conreads. Of these, structures in 270 conreads overlap with existing predictions in human. To sum up, the PigEST resource comprises trans-acting elements (ncRNAs) in 715 contigs and 340 singletons as well as cis-acting elements (inside UTRs) in 311 contigs and 51 singletons, of which 18 conreads contain both predictions of trans- and cis-acting elements. The predicted RNAz candidates were compared with the PigEST expression information and we identify 114 contigs with an RNAz prediction and expression in at least ten of the non-normalised cDNA libraries. We conclude that the contigs with RNAz and known predictions are in general expressed at a much lower level than protein coding transcripts. In addition, we also observe that our ncRNA candidates constitute about one to two percent of the genes expressed in the cDNA libraries. Intriguingly, the cDNA libraries from developmental (brain) tissues contain the highest amount of ncRNA candidates, about two percent. These observations are related to existing knowledge and hypotheses about the role of ncRNAs in higher organisms. Furthermore, about 80% porcine coding transcripts (of 18,600 identified) as well as less than one-third ORF-free transcripts are conserved at least in the closely related bovine genome. Approximately one percent of the coding and 10% of the remaining matches are unique between the PigEST data and cow genome. Based on the pig-cow alignments, we searched for similarities to 16 other organisms by UCSC available alignments, which resulted in a 87% coverage by the human genome for instance. Conclusion Besides recovering several of the already annotated functional RNA structures, we predicted a large number of high confidence conserved secondary structures in polyadenylated porcine transcripts. Our observations of relatively low expression levels of predicted ncRNA candidates together with the observations of higher relative amount in cDNA libraries from developmental stages are in agreement with the current paradigm of ncRNA roles in higher organisms and supports the idea of polyadenylated ncRNAs.Published versio
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