1,356 research outputs found
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
The number of complete, publicly available genome sequences is now greater than 200, and this number is expected to rapidly grow in the near future as metagenomic and environmental sequencing efforts escalate and the cost of sequencing drops. In order to make use of this data for understanding particular organisms and for discerning general principles about how organisms function, it will be necessary to reconstruct their various biochemical reaction networks. Principal among these will be transcriptional regulatory networks. Given the physical and logical complexity of these networks, the various sources of (often noisy) data that can be utilized for their elucidation, the monetary costs involved, and the huge number of potential experiments (~10(12)) that can be performed, experiment design algorithms will be necessary for synthesizing the various computational and experimental data to maximize the efficiency of regulatory network reconstruction. This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks. It is meant to be applied iteratively in conjunction with an experimental laboratory component. The algorithm is presented here in the context of reconstructing transcriptional regulation for metabolism in Escherichia coli, and, through a retrospective analysis with previously performed experiments, we show that the produced experiment designs conform to how a human would design experiments. The algorithm is able to utilize probability estimates based on a wide range of computational and experimental sources to suggest experiments with the highest potential of discovering the greatest amount of new regulatory knowledge
Lyapunov spectra and nonequilibrium ensembles equivalence in 2D fluid mechanics
We perform numerical experiments to study the Lyapunov spectra of dynamical
systems associated with the Navier–Stokes (NS) equation in two spatial dimensions truncated over the Fourier basis. Recently new equations, called GNS equations, have been introduced and conjectured to be equivalent to the NS equations at large Reynolds numbers. The Lyapunov spectra of the NS and of the corresponding GNS systems overlap, adding evidence in favor of the conjectured equivalence already studied and partially extended in previous papers. We make use of the Lyapunov spectra to study a fluctuation relation which had been proposed to extend the “fluctuation theorem” to strongly dissipative systems. Preliminary results towards the formulation of a local version of the fluctuation formula are also presented
Monte-Carlo simulation of events with Drell-Yan lepton pairs from antiproton-proton collisions
The complete knowledge of the nucleon spin structure at leading twist
requires also addressing the transverse spin distribution of quarks, or
transversity, which is yet unexplored because of its chiral-odd nature.
Transversity can be best extracted from single-spin asymmetries in fully
polarized Drell-Yan processes with antiprotons, where valence contributions are
involved anyway. Alternatively, in single-polarized Drell-Yan the transversity
happens convoluted with another chiral-odd function, which is likely to be
responsible for the well known (and yet unexplained) violation of the Lam-Tung
sum rule in the corresponding unpolarized cross section. We present Monte-Carlo
simulations for the unpolarized and single-polarized Drell-Yan at different center-of-mass energies in both
configurations where the antiproton beam hits a fixed proton target or it
collides on another proton beam. The goal is to estimate the minimum number of
events needed to extract the above chiral-odd distributions from future
measurements at the HESR ring at GSI. It is important to study the feasibility
of such experiments at HESR in order to demonstrate that interesting spin
physics can be explored already using unpolarized antiprotons.Comment: Deeply revised text with improved discussion of kinematics and
results; added one table; 12 figures. Accepted for publication in Phys. Rev.
Propene Polymerization Promoted by C2-Symmetric Metallocene Catalysts: From Atactic to Isotactic Polypropene in Consequence of an Isotope Effect
We studied the polymerization of propene-2-d
promoted by the prototypical isotactic-specific catalyst system
rac-ethylenebis(4,5,6,7-tetrahydro-1-indenyl)ZrCl2/MAO. In
this communication, we report the results of our investigation,
documenting a large isotope effect on the balance between
polyinsertion and epimerization and, therefore, on the stereospecificity.
The mechanistic implications of such results are
also discusse
Pfaffian representations of cubic surfaces
Let K be a field of characteristic zero. We describe an algorithm which
requires a homogeneous polynomial F of degree three in K[x_0,x_1,x_2,x_3] and a
zero A of F in P^3_K and ensures a linear pfaffian representation of V(F) with
entries in K[x_0,x_1,x_2,x_3], under mild assumptions on F and A. We use this
result to give an explicit construction of (and to prove the existence of) a
linear pfaffian representation of V(F), with entries in K'[x_0,x_1,x_2,x_3],
being K' an algebraic extension of K of degree at most six. An explicit example
of such a construction is given.Comment: 17 pages. Expanded with some remarks. Published with minor
corrections in Geom. Dedicat
Free-energy transition in a gas of non-interacting nonlinear wave-particles
We investigate the dynamics of a gas of non-interacting particle-like soliton
waves, demonstrating that phase transitions originate from their collective
behavior. This is predicted by solving exactly the nonlinear equations and by
employing methods of the statistical mechanics of chaos. In particular, we show
that a suitable free energy undergoes a metamorphosis as the input excitation
is increased, thereby developing a first order phase transition whose
measurable manifestation is the formation of shock waves. This demonstrates
that even the simplest phase-space dynamics, involving independent (uncoupled)
degrees of freedom, can sustain critical phenomena.Comment: 4 pages, 3 figure
Surfaces containing a family of plane curves not forming a fibration
We complete the classification of smooth surfaces swept out by a
1-dimensional family of plane curves that do not form a fibration. As a
consequence, we characterize manifolds swept out by a 1-dimensional family of
hypersurfaces that do not form a fibration.Comment: Author's post-print, final version published online in Collect. Mat
Il patrimonio culturale e paesaggistico per lo sviluppo locale
Il contributo tematizza il ruolo delle Fondazioni Bancarie nel sostegno e nella promozione di progetti di sviluppo locale basati sul patrimonio culturale e paesaggistico
- …