18,804 research outputs found
Scaling laws for molecular communication
In this paper, we investigate information-theoretic scaling laws, independent
from communication strategies, for point-to-point molecular communication,
where it sends/receives information-encoded molecules between nanomachines.
Since the Shannon capacity for this is still an open problem, we first derive
an asymptotic order in a single coordinate, i.e., i) scaling time with constant
number of molecules and ii) scaling molecules with constant time . For a
single coordinate case, we show that the asymptotic scaling is logarithmic in
either coordinate, i.e., and , respectively.
We also study asymptotic behavior of scaling in both time and molecules and
show that, if molecules and time are proportional to each other, then the
asymptotic scaling is linear, i.e., .Comment: Accepted for publication in the 2014 IEEE International Symposium on
Information Theor
Probing the limits to microRNA-mediated control of gene expression
According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators
of an effective positive interaction between long coding or non-coding RNA
molecules, carrying significant potential implications for a variety of
biological processes. Here, inspired by recent work providing a quantitative
description of small regulatory elements as information-conveying channels, we
characterize the effectiveness of miRNA-mediated regulation in terms of the
optimal information flow achievable between modulator (transcription factors)
and target nodes (long RNAs). Our findings show that, while a sufficiently
large degree of target derepression is needed to activate miRNA-mediated
transmission, (a) in case of differential mechanisms of complex processing
and/or transcriptional capabilities, regulation by a post-transcriptional
miRNA-channel can outperform that achieved through direct transcriptional
control; moreover, (b) in the presence of large populations of weakly
interacting miRNA molecules the extra noise coming from titration disappears,
allowing the miRNA-channel to process information as effectively as the direct
channel. These observations establish the limits of miRNA-mediated
post-transcriptional cross-talk and suggest that, besides providing a degree of
noise buffering, this type of control may be effectively employed in cells both
as a failsafe mechanism and as a preferential fine tuner of gene expression,
pointing to the specific situations in which each of these functionalities is
maximized.Comment: 16 page
Molecular Communication Using Brownian Motion with Drift
Inspired by biological communication systems, molecular communication has
been proposed as a viable scheme to communicate between nano-sized devices
separated by a very short distance. Here, molecules are released by the
transmitter into the medium, which are then sensed by the receiver. This paper
develops a preliminary version of such a communication system focusing on the
release of either one or two molecules into a fluid medium with drift. We
analyze the mutual information between transmitter and the receiver when
information is encoded in the time of release of the molecule. Simplifying
assumptions are required in order to calculate the mutual information, and
theoretical results are provided to show that these calculations are upper
bounds on the true mutual information. Furthermore, optimized degree
distributions are provided, which suggest transmission strategies for a variety
of drift velocities.Comment: 20 pages, 7 figures, Accepted for publication in IEEE Trans. on
NanoBioscienc
Optimal Receiver Design for Diffusive Molecular Communication With Flow and Additive Noise
In this paper, we perform receiver design for a diffusive molecular
communication environment. Our model includes flow in any direction, sources of
information molecules in addition to the transmitter, and enzymes in the
propagation environment to mitigate intersymbol interference. We characterize
the mutual information between receiver observations to show how often
independent observations can be made. We derive the maximum likelihood sequence
detector to provide a lower bound on the bit error probability. We propose the
family of weighted sum detectors for more practical implementation and derive
their expected bit error probability. Under certain conditions, the performance
of the optimal weighted sum detector is shown to be equivalent to a matched
filter. Receiver simulation results show the tradeoff in detector complexity
versus achievable bit error probability, and that a slow flow in any direction
can improve the performance of a weighted sum detector.Comment: 14 pages, 7 figures, 1 appendix. To appear in IEEE Transactions on
NanoBioscience (submitted July 31, 2013, revised June 18, 2014, accepted July
7, 2014
Estimation and reduction of the uncertainties in chemical models: Application to hot core chemistry
It is not common to consider the role of uncertainties in the rate
coefficients used in interstellar gas-phase chemical models. In this paper, we
report a new method to determine both the uncertainties in calculated molecular
abundances and their sensitivities to underlying uncertainties in the kinetic
data utilized. The method is used in hot core models to determine if previous
analyses of the age and the applicable cosmic-ray ionization rate are valid. We
conclude that for young hot cores ( yr), the modeling uncertainties
related to rate coefficients are reasonable so that comparisons with
observations make sense. On the contrary, the modeling of older hot cores is
characterized by strong uncertainties for some of the important species. In
both cases, it is crucial to take into account these uncertainties to draw
conclusions from the comparison of observations with chemical models.Comment: Accepted for publication in A&
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Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.
The regulation of transcription requires the coordination of numerous activities on DNA, yet how transcription factors mediate these activities remains poorly understood. Here, we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos to study the nuclear organization and interactions of the key transcription factors Zelda and Bicoid. In contrast to previous studies suggesting stable, cooperative binding, we show that both factors interact with DNA with surprisingly high off-rates. We find that both factors form dynamic subnuclear hubs, and that Bicoid binding is enriched within Zelda hubs. Remarkably, these hubs are both short lived and interact only transiently with sites of active Bicoid-dependent transcription. Based on our observations, we hypothesize that, beyond simply forming bridges between DNA and the transcription machinery, transcription factors can organize other proteins into hubs that transiently drive multiple activities at their gene targets.Editorial noteThis article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter)
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