Two novel aspects of the kinetics of gene expression including miRNAs

Open Physics ◽  
2013 ◽  
Vol 11 (4) ◽  
Author(s):  
Vladimir Zhdanov
Keyword(s):  
Small Rnas ◽  
Noncoding Rna ◽  
Regulatory Protein ◽  
Experimental Studies ◽  
Kinetic Equations ◽  
Mean Field ◽  
Mrna Translation ◽  
The Mean ◽  
Non Coding Rnas ◽  
Kinetics Of

AbstractIn eukaryotic cells, many genes are transcribed into non-coding RNAs. Small RNAs or, more specifically, microRNAs (miRNAs) form an abundant sub-class of such RNAs. miRNAs are transcribed as long noncoding RNA and then generated via a processing pathway down to the 20–24-nucleotide length. The key ability of miRNAs is to associate with target mRNAs and to suppress their translation and/or facilitate degradation. Using the mean-field kinetic equations and Monte Carlo simulations, we analyze two aspects of this interplay. First, we describe the situation when the formation of mRNA or miRNA is periodically modulated by a transcription factor which itself is not perturbed by these species. Depending on the ratio between the mRNA and miRNA formation rates, the corresponding induced periodic kinetics are shown to be either nearly harmonic or shaped as anti-phase pulses. The second part of the work is related to recent experimental studies indicating that differentiation of stem cells often involves changes in gene transcription into miRNAs and/or the interference between miRNAs, mRNAs and proteins. In particular, the regulatory protein obtained via mRNA translation may suppress the miRNA formation, and the latter may suppress in turn the miRNA-mRNA association and degradation. The corresponding bistable kinetics are described in detail.

scholarly journals Neutrino quantum kinetic equations

2015 ◽  
Vol 24 (09) ◽  
pp. 1541009 ◽  
Author(s):  
Cristina Volpe
Keyword(s):  
Evolution Equations ◽  
Kinetic Equations ◽  
Mean Field ◽  
Boltzmann Equations ◽  
The Mean ◽  
Salient Features ◽  
Neutrino Propagation

Neutrinos propagate in astrophysical and cosmological environments modifying their flavor in intriguing ways. The study of neutrino propagation in media is based on the mean-field, extended mean-field and Boltzmann equations. We summarize salient features of these evolution equations and the methods employed so far to derive them. We emphasize applications to situations of observational interest.

scholarly journals Metazoan tsRNAs: Biogenesis, Evolution and Regulatory Functions

2019 ◽  
Vol 5 (1) ◽  
pp. 18 ◽  
Author(s):  
Shengqian Dou ◽  
Yirong Wang ◽  
Jian Lu
Keyword(s):  
Small Rnas ◽  
Mrna Translation ◽  
Evolutionary Genomics ◽  
Biological Processes ◽  
Domains Of Life ◽  
Conservation Patterns ◽  
Fundamental Biology ◽  
Non Coding Rnas ◽  
Regulatory Functions ◽  
Post Transcriptional Regulation

Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory non-coding RNAs that play important roles in post-transcriptional regulation across a variety of biological processes. Here, we review the recent advances in tsRNA biogenesis and regulatory functions from the perspectives of functional and evolutionary genomics, with a focus on the tsRNA biology of Drosophila. We first summarize our current understanding of the biogenesis mechanisms of different categories of tsRNAs that are generated under physiological or stressed conditions. Next, we review the conservation patterns of tsRNAs in all domains of life, with an emphasis on the conservation of tsRNAs between two Drosophila species. Then, we elaborate the currently known regulatory functions of tsRNAs in mRNA translation that are independent of, or dependent on, Argonaute (AGO) proteins. We also highlight some issues related to the fundamental biology of tsRNAs that deserve further study.

scholarly journals Some aspects of the inertial spin model for flocks and related kinetic equations

2020 ◽  
Vol 30 (10) ◽  
pp. 1987-2022 ◽  
Author(s):  
D. Benedetto ◽  
P. Buttà ◽  
E. Caglioti
Keyword(s):  
Thermal Noise ◽  
Kinetic Equations ◽  
Mean Field ◽  
Planck Equation ◽  
Dynamical Variable ◽  
Spin Model ◽  
Field Limit ◽  
Mean Field Limit ◽  
Macroscopic Behavior ◽  
The Mean

In this paper, we study the macroscopic behavior of the inertial spin (IS) model. This model has been recently proposed to describe the collective dynamics of flocks of birds, and its main feature is the presence of an auxiliary dynamical variable, a sort of internal spin, which conveys the interaction among the birds with the effect of better describing the turning of flocks. After discussing the geometrical and mechanical properties of the IS model, we show that, in the case of constant interaction among the birds, its mean-field limit is described by a nonlinear Fokker–Planck equation, whose equilibria are fully characterized. Finally, in the case of non-constant interactions, we derive the kinetic equation for the mean-field limit of the model in the absence of thermal noise, and explore its macroscopic behavior by analyzing the mono-kinetic solutions.

NON-ABELIAN PERMITTIVITY OF QUARK–GLUON PLASMA DUE TO THE SELF-INTERACTION OF FIELD

2000 ◽  
Vol 15 (30) ◽  
pp. 1843-1849 ◽  
Author(s):  
JI-SHENG CHEN ◽  
JIA-RONG LI
Keyword(s):  
Quark Gluon Plasma ◽  
Kinetic Equations ◽  
Mean Field ◽  
Gluon Plasma ◽  
Nonlinear Frequency ◽  
Leading Order ◽  
Coupling Constant ◽  
The Mean ◽  
Color Field ◽  
Mean Field Equation

From the semiclassical kinetic equations and the mean field equation of quark–gluon plasma, the contribution of the color field self-coupling to the non-Abelian permittivity at the leading order in the weak coupling constant is analyzed. The nonlinear frequency drift has been estimated for the k=0 modes.

Simulation of Precipitates Evolution in Steels with V and Nb at Annealing

2015 ◽  
Vol 3 ◽  
pp. 167-180
Author(s):  
I.I. Gorbachev ◽  
Vladimir V. Popov ◽  
A.Yu. Pasynkov
Keyword(s):  
Mean Field ◽  
Dissolution Kinetics ◽  
Field Approximation ◽  
Numerical Realization ◽  
Mean Field Approximation ◽  
The Mean ◽  
Kinetics Of

Based on the mean field approximation, a model has been worked out for the description of evolution of carbonitride precipitate ensemble with various composition in steels at the stages of their growth, dissolution and coarsening. Based on the numerical realization of this model, the calculations of growth and dissolution kinetics of carbonitrides in a Fe-Nb-V-C-N system have been carried out.

scholarly journals Making ends meet: new functions of mRNA secondary structure

2020 ◽  
Author(s):  
Dmitri N. Ermolenko ◽  
David Mathews
Keyword(s):  
Secondary Structure ◽  
Translation Initiation ◽  
Protein Complexes ◽  
Experimental Studies ◽  
Mrna Translation ◽  
Low Complexity ◽  
Mrna Secondary Structure ◽  
Protein Coding ◽  
Random Coils ◽  
Non Coding Rnas

AbstractThe 5’ cap and 3’ poly(A) tail of mRNA are known to synergistically regulate mRNA translation and stability. Recent computational and experimental studies revealed that both protein-coding and non-coding RNAs will fold with extensive intramolecular secondary structure, which will result in close distances between the sequence ends. This proximity of the ends is a sequence-independent, universal property of most RNAs. Only low-complexity sequences without guanosines are without secondary structure and exhibit end-to-end distances expected for RNA random coils. The innate proximity of RNA ends might have important biological implications that remain unexplored. In particular, the inherent compactness of mRNA might regulate translation initiation by facilitating the formation of protein complexes that bridge mRNA 5’ and 3’ ends. Additionally, the proximity of mRNA ends might mediate coupling of 3′ deadenylation to 5′ end mRNA decay.

KINETICS OF MIGRATION AND COALESCENCE OF SUPPORTED NM-SIZED METAL PARTICLES

2008 ◽  
Vol 15 (03) ◽  
pp. 217-220 ◽  
Author(s):  
VLADIMIR P. ZHDANOV
Keyword(s):  
Particle Size ◽  
Monte Carlo ◽  
Mean Field ◽  
Metal Particles ◽  
Fourth Power ◽  
Average Value ◽  
The Mean ◽  
Kinetics Of ◽  
Size Distribution Of Particles ◽  
Good Agreement

Monte Carlo simulations of the kinetics of migration and coalescence of nm-sized metal particles on a uniform surface and a surface with traps in the physically reasonable case when the diffusion coefficient of particles varies inversely as the fourth power of the particle size are presented. The Monte Carlo kinetics are demonstrated to be in good agreement with the mean-field results. The size distribution of particles is found to be nearly symmetrical with respect to the average value.

Modelling of Copper Precipitation in Fe-Cu Alloys Under Irradiation

2000 ◽  
Vol 650 ◽  
Author(s):  
Alexander V. Barashev ◽  
Stanislav I. Golubov ◽  
David J. Bacon
Keyword(s):  
Ostwald Ripening ◽  
Experimental Studies ◽  
Mean Field ◽  
Precipitate Size ◽  
Copper Precipitation ◽  
Cu Alloys ◽  
Main Effect ◽  
Pressure Vessel Steels ◽  
The Mean ◽  
Reactor Pressure

ABSTRACTPrecipitation of copper-rich clusters is a major cause of in-service hardening of reactor pressure vessel steels and has attracted much attention. Experimental studies of microstructural changes in alloys under various conditions have revealed similarities and differences. It has been established that under ageing the precipitate ensemble experiences normal nucleation, growth and Ostwald ripening, a distinguishing feature of which is the bcc-9R-3R-fcc transformations the precipitates undergo during growth. The main effect of electron irradiation is believed to be enhancement of the diffusion of copper and hence acceleration of the kinetics. In the case of neutron irradiation, however, there are many aspects that are not clear. One is that at temperatures less than about 300°C the precipitate size is observed to be very small (∼1-3 nm), i.e. the coarsening rate is very low. In this paper we study this phenomenon by computer simulations based on the “mean-field” approach for describing microstructural evolution.

scholarly journals Experimental and Theoretical Investigation of Microdischarge Plasma in the Vortex Gas Flow

2020 ◽  
Vol 7 (1) ◽  
pp. 1-5
Author(s):  
V. Chernyak ◽  
O. Kolomiiets ◽  
O. Prysiazhna ◽  
O. Tsimbalyuk ◽  
V. Iukhymenko ◽  
...  
Keyword(s):  
Electric Field ◽  
Gas Flow ◽  
Vortex Flow ◽  
Microwave Plasma ◽  
Experimental Studies ◽  
Computer Code ◽  
Gas Temperature ◽  
Electrical Parameters ◽  
The Mean ◽  
Kinetics Of

Experimental studies of the electrical parameters of the microdischarge and the plasma of the microdischarge in the vortex flow of CO<sub>2</sub> as the plasma-forming gas was carried out. The kinetics of the formation of some components of microwave plasma was considered using ZDPlasKin computer code and Bolsig+ at experimentally measured electric field strengths, pressure and gas temperature. The key reactions of microdischarge were determined. The Bolsig+ code was used to determine the mean energy of electrons.

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