44 research outputs found
Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mRNA translation
Messenger RNA translation is often studied by means of statistical-mechanical
models based on the Asymmetric Simple Exclusion Process (ASEP), which considers
hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In
this work we extend this class of models and consider the two fundamental steps
of the ribosome's biochemical cycle following a coarse-grained perspective. In
order to achieve a better understanding of the underlying biological processes
and compare the theoretical predictions with experimental results, we provide a
description lying between the minimal ASEP-like models and the more detailed
models, which are analytically hard to treat. We use a mean-field approach to
study the dynamics of particles associated with an internal stepping cycle. In
this framework it is possible to characterize analytically different phases of
the system (high density, low density or maximal current phase). Crucially, we
show that the transitions between these different phases occur at different
parameter values than the equivalent transitions in a standard ASEP, indicating
the importance of including the two fundamental steps of the ribosome's
biochemical cycle into the model.Comment: 9 pages, 9 figure
Feedback topology and XOR-dynamics in Boolean networks with varying input structure
We analyse a model of fixed in-degree Random Boolean Networks in which the
fraction of input-receiving nodes is controlled by a parameter gamma. We
investigate analytically and numerically the dynamics of graphs under a
parallel XOR updating scheme. This scheme is interesting because it is
accessible analytically and its phenomenology is at the same time under
control, and as rich as the one of general Boolean networks. Biologically, it
is justified on abstract grounds by the fact that all existing interactions
play a dynamical role. We give analytical formulas for the dynamics on general
graphs, showing that with a XOR-type evolution rule, dynamic features are
direct consequences of the topological feedback structure, in analogy with the
role of relevant components in Kauffman networks. Considering graphs with fixed
in-degree, we characterize analytically and numerically the feedback regions
using graph decimation algorithms (Leaf Removal). With varying gamma, this
graph ensemble shows a phase transition that separates a tree-like graph region
from one in which feedback components emerge. Networks near the transition
point have feedback components made of disjoint loops, in which each node has
exactly one incoming and one outgoing link. Using this fact we provide
analytical estimates of the maximum period starting from topological
considerations
The Dynamics of Supply and Demand in mRNA Translation
We study the elongation stage of mRNA translation in eukaryotes and find that, in contrast to the assumptions of previous models, both the supply and the demand for tRNA resources are important for determining elongation rates. We find that increasing the initiation rate of translation can lead to the depletion of some species of aa-tRNA, which in turn can lead to slow codons and queueing. Particularly striking “competition” effects are observed in simulations of multiple species of mRNA which are reliant on the same pool of tRNA resources. These simulations are based on a recent model of elongation which we use to study the translation of mRNA sequences from the Saccharomyces cerevisiae genome. This model includes the dynamics of the use and recharging of amino acid tRNA complexes, and we show via Monte Carlo simulation that this has a dramatic effect on the protein production behaviour of the system
Efficient Modelling of the Near Field Coupling Between Phased Array Antennas
In this contribution we present an accurate modelling of the coupling between two patch array structures which act as transmitting and receiving antenna in a 24GHz near range sensor system. the EM analysis is performed by means of the efficient transmission line matrix-integral equation (TLM-IE) method which permits to model exact radiating boundary conditions. The calculated return-loss and mutual near field coupling between the antennas is investigated and compared to measured result
Analysis of Sensitivity for Low-Pass Multilayer Optical Filters
Integrated optical and millimetric circuits produced by standard thin film-based technology suffer from manufacturing imperfections resulting in degradation of the absorption/diffraction response. Deposition through rf-bias sputtering is of particular interest in order to design an optical multilayered (Si and SiO2) filter. Geometrical imperfections like roughness at layer boundaries however gradually increase with the number of deposited layers. The low-pass filter specifications present high sensitivity to the errors of the exact values of ideal thickness and of ideal refractive indices. In this contribution, we evaluate the sensitivity of the specifications with respect to deviation from the exact values of refractive indices and thicknesses
Development of a novel full-wave 3D-solver for the analysis of MMIC and optical integrated circuits
We introduce a novel EM solver for the accurate analysis of complex problems in the areas of MMIC and optical integrated circuits. The basic idea is to construct a unique tool which involves two efficient 3D full-wave methods, GTRD (generalized transverse resonance diffraction) and TLMIE (transmission line matrix integral equation), acting in the frequency and time domains, respectively. This tool is integrated in EM3DS, an existing tool based on the GTRD method, and is equipped with a user-friendly graphic interface and pre/post-processing instruments. The accuracy of the solver is demonstrated by modeling complex structures like MEMS, RF-package and photonic band ga