144 research outputs found
Polarons with a twist
We consider a polaron model where molecular \emph{rotations} are important.
Here, the usual hopping between neighboring sites is affected directly by the
electron-phonon interaction via a {\em twist-dependent} hopping amplitude. This
model may be of relevance for electronic transport in complex molecules and
polymers with torsional degrees of freedom, such as DNA, as well as in
molecular electronics experiments where molecular twist motion is significant.
We use a tight-binding representation and find that very different polaronic
properties are already exhibited by a two-site model -- these are due to the
nonlinearity of the restoring force of the twist excitations, and of the
electron-phonon interaction in the model. In the adiabatic regime, where
electrons move in a {\em low}-frequency field of twisting-phonons, the
effective splitting of the energy levels increases with coupling strength. The
bandwidth in a long chain shows a power-law suppression with coupling, unlike
the typical exponential dependence due to linear phonons.Comment: revtex4 source and one eps figur
Lichenometric dating (lichenometry) and the biology of the lichen genus rhizocarpon:challenges and future directions
Lichenometric dating (lichenometry) involves the use of lichen measurements to estimate the age of exposure of various substrata. Because of low radial growth rates and considerable longevity, species of the crustose lichen genus Rhizocarpon have been the most useful in lichenometry. The primary assumption of lichenometry is that colonization, growth and mortality of Rhizocarpon are similar on surfaces of known and unknown age so that the largest thalli present on the respective faces are of comparable age. This review describes the current state of knowledge regarding the biology of Rhizocarpon and considers two main questions: (1) to what extent does existing knowledge support this assumption; and (2) what further biological observations would be useful both to test its validity and to improve the accuracy of lichenometric dates? A review of the Rhizocarpon literature identified gaps in knowledge regarding early development, the growth rate/size curve, mortality, regeneration, competitive effects, colonization, and succession on rock surfaces. The data suggest that these processes may not be comparable on different rock surfaces, especially in regions where growth rates and thallus turnover are high. In addition, several variables could differ between rock surfaces and influence maximum thallus size, including rate and timing of colonization, radial growth rates, environmental differences, thallus fusion, allelopathy, thallus mortality, colonization and competition. Comparative measurements of these variables on surfaces of known and unknown age may help to determine whether the basic assumptions of lichenometry are valid. Ultimately, it may be possible to take these differences into account when interpreting estimated dates
Unexpected circular radio objects at high Galactic latitude
Large scale structure and cosmolog
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism
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