1,643 research outputs found
Enhancement of the stability of genetic switches by overlapping upstream regulatory domains
We study genetic switches formed from pairs of mutually repressing operons.
The switch stability is characterised by a well defined lifetime which grows
sub-exponentially with the number of copies of the most-expressed transcription
factor, in the regime accessible by our numerical simulations. The stability
can be markedly enhanced by a suitable choice of overlap between the upstream
regulatory domains. Our results suggest that robustness against biochemical
noise can provide a selection pressure that drives operons, that regulate each
other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX
Analytical study of an exclusive genetic switch
The nonequilibrium stationary state of an exclusive genetic switch is
considered. The model comprises two competing species and a single binding site
which, when bound to by a protein of one species, causes the other species to
be repressed. The model may be thought of as a minimal model of the power
struggle between two competing parties. Exact solutions are given for the
limits of vanishing binding/unbinding rates and infinite binding/unbinding
rates. A mean field theory is introduced which is exact in the limit of
vanishing binding/unbinding rates. The mean field theory and numerical
simulations reveal that generically bistability occurs and the system is in a
symmetry broken state. An exact perturbative solution which in principle allows
the nonequilibrium stationary state to be computed is also developed and
computed to first and second order.Comment: 28 pages, 6 figure
Maximizing Maximal Angles for Plane Straight-Line Graphs
Let be a plane straight-line graph on a finite point set
in general position. The incident angles of a vertex
of are the angles between any two edges of that appear consecutively in
the circular order of the edges incident to .
A plane straight-line graph is called -open if each vertex has an
incident angle of size at least . In this paper we study the following
type of question: What is the maximum angle such that for any finite set
of points in general position we can find a graph from a certain
class of graphs on that is -open? In particular, we consider the
classes of triangulations, spanning trees, and paths on and give tight
bounds in most cases.Comment: 15 pages, 14 figures. Apart of minor corrections, some proofs that
were omitted in the previous version are now include
Vibrational Enhancement of the Effective Donor - Acceptor Coupling
The paper deals with a simple three sites model for charge transfer phenomena
in an one-dimensional donor (D) - bridge (B) - acceptor (A) system coupled with
vibrational dynamics of the B site. It is found that in a certain range of
parameters the vibrational coupling leads to an enhancement of the effective
donor - acceptor electronic coupling as a result of the formation of the
polaron on the B site. This enhancement of the charge transfer efficiency is
maximum at the resonance, where the effective energy of the fluctuating B site
coincides with the donor (acceptor) energy.Comment: 5 pages, 3 figure
On the Complexity of Searching in Trees: Average-case Minimization
We focus on the average-case analysis: A function w : V -> Z+ is given which
defines the likelihood for a node to be the one marked, and we want the
strategy that minimizes the expected number of queries. Prior to this paper,
very little was known about this natural question and the complexity of the
problem had remained so far an open question.
We close this question and prove that the above tree search problem is
NP-complete even for the class of trees with diameter at most 4. This results
in a complete characterization of the complexity of the problem with respect to
the diameter size. In fact, for diameter not larger than 3 the problem can be
shown to be polynomially solvable using a dynamic programming approach.
In addition we prove that the problem is NP-complete even for the class of
trees of maximum degree at most 16. To the best of our knowledge, the only
known result in this direction is that the tree search problem is solvable in
O(|V| log|V|) time for trees with degree at most 2 (paths).
We match the above complexity results with a tight algorithmic analysis. We
first show that a natural greedy algorithm attains a 2-approximation.
Furthermore, for the bounded degree instances, we show that any optimal
strategy (i.e., one that minimizes the expected number of queries) performs at
most O(\Delta(T) (log |V| + log w(T))) queries in the worst case, where w(T) is
the sum of the likelihoods of the nodes of T and \Delta(T) is the maximum
degree of T. We combine this result with a non-trivial exponential time
algorithm to provide an FPTAS for trees with bounded degree
Fluctuations in Gene Regulatory Networks as Gaussian Colored Noise
The study of fluctuations in gene regulatory networks is extended to the case
of Gaussian colored noise. Firstly, the solution of the corresponding Langevin
equation with colored noise is expressed in terms of an Ito integral. Then, two
important lemmas concerning the variance of an Ito integral and the covariance
of two Ito integrals are shown. Based on the lemmas, we give the general
formulae for the variances and covariance of molecular concentrations for a
regulatory network near a stable equilibrium explicitly. Two examples, the gene
auto-regulatory network and the toggle switch, are presented in details. In
general, it is found that the finite correlation time of noise reduces the
fluctuations and enhances the correlation between the fluctuations of the
molecular components.Comment: 10 pages, 4 figure
A Hierarchical Hybrid Architecture for Mission-Oriented Robot Control
The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-03413-3_26In this work is presented a general architecture for a multi
physical agent network system based on the coordination and the behaviour
management. The system is organised in a hierarchical structure
where are distinguished the individual agent actions and the collective
ones linked to the whole agent network. Individual actions are also organised
in a hybrid layered system that take advantages from reactive and
deliberative control. Sensing system is involved as well in the behaviour
architecture improving the information acquisition performance.This work has been partially supported by the Spanish Ministry of Economy and Competitiveness under the CICYT project Mission Based Control (COBAMI): DPI2011-28507-C02-02, under coordinated project High Integrity Partitioned Embedded Systems (Hi-PartES): TIN2011-28567-C03-03, and under the collaborative research project supported by the European Union MultiPARTES Project: FP7-ICT 287702. 2011-14.Muñoz Alcobendas, M.; Munera SĂĄnchez, E.; Blanes Noguera, F.; SimĂł Ten, JE. (2013). A Hierarchical Hybrid Architecture for Mission-Oriented Robot Control. En ROBOT2013: First Iberian Robotics Conference: Advances in Robotics, Vol. 1. Springer. 363-380. https://doi.org/10.1007/978-3-319-03413-3_26S363380Aragues, R.: Consistent data association in multi-robot systems with limited communications. 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A tight lower bound for steiner orientation
In the STEINER ORIENTATION problem, the input is a mixed graph G (it has both directed and undirected edges) and a set of k terminal pairs T. The question is whether we can orient the undirected edges in a way such that there is a directed sât path for each terminal pair (s,t)âT. Arkin and Hassin [DAMâ02] showed that the STEINER ORIENTATION problem is NP-complete. They also gave a polynomial time algorithm for the special case when k=2
.
From the viewpoint of exact algorithms, Cygan, Kortsarz and Nutov [ESAâ12, SIDMAâ13] designed an XP algorithm running in nO(k) time for all kâ„1. Pilipczuk and Wahlström [SODA â16] showed that the STEINER ORIENTATION problem is W[1]-hard parameterized by k. As a byproduct of their reduction, they were able to show that under the Exponential Time Hypothesis (ETH) of Impagliazzo, Paturi and Zane [JCSSâ01] the STEINER ORIENTATION problem does not admit an f(k)â
no(k/logk) algorithm for any computable function f. That is, the nO(k) algorithm of Cygan et al. is almost optimal.
In this paper, we give a short and easy proof that the nO(k) algorithm of Cygan et al. is asymptotically optimal, even if the input graph has genus 1. Formally, we show that the STEINER ORIENTATION problem is W[1]-hard parameterized by the number k of terminal pairs, and, under ETH, cannot be solved in f(k)â
no(k) time for any function f even if the underlying undirected graph has genus 1. We give a reduction from the GRID TILING problem which has turned out to be very useful in proving W[1]-hardness of several problems on planar graphs. As a result of our work, the main remaining open question is whether STEINER ORIENTATION admits the âsquare-root phenomenonâ on planar graphs (graphs with genus 0): can one obtain an algorithm running in time f(k)â
nO(kâ) for PLANAR STEINER ORIENTATION, or does the lower bound of f(k)â
no(k) also translate to planar graphs
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