1,426 research outputs found
Spin-models of granular compaction: From one-dimensional models to random graphs
We discuss two athermal types of dynamics suitable for spin-models designed
to model repeated tapping of a granular assembly. These dynamics are applied to
a range of models characterised by a 3-spin Hamiltonian aiming to capture the
geometric frustration in packings of granular matter.Comment: Contribution to "Challenges in Granular Media", ICTP Trieste; to
appear in 'Advances in Complex Systems
Direct application of UNIFAC activity coefficient computer programs to the calculation of solvent activities and .chi.-parameters for polymer solutions
Application of UNIFAC computer calculations to polymer solutions does not seem to make sense because of the value of the solvent activity: close to 1.000 over a considerable range of concentrations (up to 90% of polymer). A simple procedure is proposed to calculate solvent activity coefficients, and thus X-parameters, such that the easily available UNIFAC computer programs may be applied directly, without any modification
Quantitative analysis of competition in post-transcriptional regulation reveals a novel signature in target expression variation
When small RNAs are loaded onto Argonaute proteins they can form the
RNA-induced silencing complexes (RISCs), which mediate RNA interference.
RISC-formation is dependent on a shared pool of Argonaute proteins and RISC
loading factors, and is thus susceptible to competition among small RNAs for
loading. We present a mathematical model that aims to understand how small RNA
competition for the PTR resources affects target gene repression. We discuss
that small RNA activity is limited by RISC-formation, RISC-degradation and the
availability of Argonautes. Together, these observations explain a number of
PTR saturation effects encountered experimentally. We show that different
competition conditions for RISC-loading result in different signatures of PTR
activity determined also by the amount of RISC-recycling taking place. In
particular, we find that the small RNAs less efficient at RISC-formation, using
fewer resources of the PTR pathway, can perform in the low RISC-recycling range
equally well as their more effective counterparts. Additionally, we predict a
novel signature of PTR in target expression levels. Under conditions of low
RISC-loading efficiency and high RISC-recycling, the variation in target levels
increases linearly with the target transcription rate. Furthermore, we show
that RISC-recycling determines the effect that Argonaute scarcity conditions
have on target expression variation. Our observations taken together offer a
framework of predictions which can be used in order to infer from experimental
data the particular characteristics of underlying PTR activity.Comment: 23 pages, 3 Figures, accepted for publication to the Biophysical
Journa
Adaptive evolution of transcription factor binding sites
The regulation of a gene depends on the binding of transcription factors to
specific sites located in the regulatory region of the gene. The generation of
these binding sites and of cooperativity between them are essential building
blocks in the evolution of complex regulatory networks. We study a theoretical
model for the sequence evolution of binding sites by point mutations. The
approach is based on biophysical models for the binding of transcription
factors to DNA. Hence we derive empirically grounded fitness landscapes, which
enter a population genetics model including mutations, genetic drift, and
selection. We show that the selection for factor binding generically leads to
specific correlations between nucleotide frequencies at different positions of
a binding site. We demonstrate the possibility of rapid adaptive evolution
generating a new binding site for a given transcription factor by point
mutations. The evolutionary time required is estimated in terms of the neutral
(background) mutation rate, the selection coefficient, and the effective
population size. The efficiency of binding site formation is seen to depend on
two joint conditions: the binding site motif must be short enough and the
promoter region must be long enough. These constraints on promoter architecture
are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive
evolution of genetic switches and of signal integration through binding
cooperativity between different sites. Experimental tests of this picture
involving the statistics of polymorphisms and phylogenies of sites are
discussed.Comment: published versio
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