Showing papers by "Alexander M. Samsonov published in 2015"

Numerical Analysis of Particle Trajectories in Living Cells under Uncertainty Conditions

Abstract: We have developed a numerical method for the analysis of particle trajectories in living cells, where a type of movement is determined by Akaike's information criterion, while model parameters are identified by a weighted least squares method. The method is realized in computer software, written in the Java programming language, that enables us to automatically conduct the analysis of trajectories. The method is tested on synthetic trajectories with known parameters, and applied to the analysis of replication complexes in cells, infected with hepatitis C virus. Results of the analysis are in agreement with available data on the movement of biological objects along microtubules.

Rapid detection of delamination areas in laminated structural elements by means of optically monitored strain solitons

Abstract: Modern structural elements are often made of laminated polymer materials or composites on the base of polymer matrices. The proper functioning of these elements may be of vital importance especially in automotive and aerospace industries, in gas and oil transportation. The major problem in their performance is a possibility of a sudden and irreversible delamination caused by various factors. We propose and study a NDT approach aimed to detect delamination areas in adhesively bonded layered structural elements made of different materials. The proposed approach is evaluated by use of holographic detection and monitoring of the evolution of bulk strain solitons generated in such structures.

The dynamics of a feed-forward loop depends on the regulator type in its indirect pathway

Abstract: Gene networks frequently contain a motif with a feed-forward loop, in which a transcription factor regulates target-gene expression both directly and indirectly via another regulator that also controls the target gene. The results of mathematical modeling of the feed-forward loops with either transcription factor or miRNA as a repressor in the indirect pathway are described. The behavior of such loops in time has been studied. As has been shown, replacement of the second transcription factor with miRNA changes the dynamics of feed-forward loops, conferring new properties to a biological system that are critical for fine tuning of its functions.

A model for the expression of gap genes based on the Jeffreys-type equation.

Abstract: MOTIVATION We propose the third-order model equation of the Jeffreys type for concentrations of gap gene proteins in order to take into account particle inertia. Gap genes are responsible for formation of body segments in Drosophila melanogaster embryo during its early development. Usually the expression of the genes is described by the model of protein transport based on conventional diffusion equation. However, the model is known to govern the Brownian (non-inertial) motion of particles; hence, it is hardly applicable to the description of protein transport. RESULTS Analysis of the Jeffreys-type equation results in the necessary condition for the problem to be well-posed. Application of the Jeffreys-type equation with non-linear terms to description of the dynamics of gap gene network demonstrates better fitting to experimental data than the conventional model. AVAILABILITY AND IMPLEMENTATION Implementation of solver algorithms and the software are freely available from: https://github.com/wswgG/solver-for-the-Jeffreys-type-equations-system .

Method of Entirely Parallel Differential Evolution for Model Adaptation in Systems Biology

Abstract: We developed a method of entirely parallel differential evolution for identification of unknown parameters of mathematical models by minimization of the objective function that describes the discrepancy of the model solution and the experimental data. The method is implemented in the free and open source software available on the Internet. The method demonstrated a good performance comparable to the top three methods from CEC-2014 and was successfully applied to several biological problems.

Dynamics of miRNA-driven feed-forward loop depends upon miRNA action mechanisms

Abstract: Background: We perform the theoretical analysis of a gene network sub-system, composed of a feed-forward loop, in which the upstream transcription factor regulates the target gene via two parallel pathways: directly, and via interaction with miRNA. Results: As the molecular mechanisms of miRNA action are not clear so far, we elaborate three mathematical models, in which miRNA either represses translation of its target or promotes target mRNA degradation, or is not re-used, but degrades along with target mRNA. We examine the feed-forward loop dynamics quantitatively at the whole time interval of cell cycle. We rigorously proof the uniqueness of solutions to the models and obtain the exact solutions in one of them analytically. Conclusions: We have shown that different mechanisms of miRNA action lead to a variety of types of dynamical behavior of feed-forward loops. In particular, we found that the ability of feed-forward loop to dampen fluctuations introduced by transcription factor is the model and parameter dependent feature. We also discuss how our results could help a biologist to infer the mechanism of miRNA action.

The differential evolution entirely parallel method for model adaptation in systems biology

Abstract: The differential evolution entirely parallel method has been developed to enable the identification of unknown parameters of mathematical models by minimization of the deviation of the solution from experimental data The method is implemented in a free open-source software that is downloadable from the Internet The results of processing of test functions showed that the accuracy of the method is comparable to that of the three best algorithms from CEC-2014 The method has been successfully used in a number of real biological problems