On insertion-deletion systems over relational words

We introduce a new notion of a relational word as a finite totally ordered set of positions endowed with three binary relations that describe which positions are labeled by equal data, by unequal data and those having an undefined relation between their labels. We define the operations of insertion and deletion on relational words generalizing corresponding operations on strings. We prove that the transitive and reflexive closure of these operations has a decidable membership problem for the case of short insertion-deletion rules (of size two/three and three/two). At the same time, we show that in the general case such systems can produce a coding of any recursively enumerable language leading to undecidabilty of reachability questions.Comment: 24 pages, 8 figure

Thermalization of coupled atom-light states in the presence of optical collisions

The interaction of a two-level atomic ensemble with a quantized single mode electromagnetic field in the presence of optical collisions (OC) is investigated both theoretically and experimentally. The main accent is made on achieving thermal equilibrium for coupled atom-light states (in particular dressed states). We propose a model of atomic dressed state thermalization that accounts for the evolution of the pseudo-spin Bloch vector components and characterize the essential role of the spontaneous emission rate in the thermalization process. Our model shows that the time of thermalization of the coupled atom-light states strictly depends on the ratio of the detuning and the resonant Rabi frequency. The predicted time of thermalization is in the nanosecond domain and about ten times shorter than the natural lifetime at full optical power in our experiment. Experimentally we are investigating the interaction of the optical field with rubidium atoms in an ultra-high pressure buffer gas cell under the condition of large atom-field detuning comparable to the thermal energy in frequency units. In particular, an observed detuning dependence of the saturated lineshape is interpreted as evidence for thermal equilibrium of coupled atom-light states. A significant modification of sideband intensity weights is predicted and obtained in this case as well.Comment: 14 pages, 12 figures; the content was edite

Simulation of geological faults with discrete element method

We present an algorithm for simulation of the Earth’s crust tectonic movements and formation of the geological faults and near-fault damage zones. The algorithms are based on the Discrete Elements Method, and it is implemented using CUDA technology. We used to simulate faults formation due to different scenarios of tectonic movements. We considered the displacements with dipping angles varied from 30 to 90 degrees; i.e., up to vertical throw. For each scenario, we performed simulations for some statistical realizations. To characterize the simulated faults and damage zones, we consider the strains distribution and apply data clustering and Karhunen-Loeve analysis to distinguish between different forms of the fault zones. In particular, clustering analysis shows that displacements with high and low dip angles form completely different geological structures. Nearly vertical displacements, high dip angles, form wide V-shaped deformation zones, whereas the at displacements cause narrow fault-cores with rapidly decreasing strains apart from the fault core. Results of the presented simulations can be used to estimate mechanical and seismic properties of rocks in the vicinity of the faults and applied further to construct models for seismic modeling and interpretation, hydrodynamical simulations, history of matching simulation, etc

High temperature phase transition in the coupled atom-light system in the presence of optical collisions

The problem of photonic phase transition for the system of a two-level atomic ensemble interacting with a quantized single-mode electromagnetic field in the presence of optical collisions (OC) is considered. We have shown that for large and negative atom-field detuning a photonic field exhibits high temperature second order phase transition to superradiant state under thermalization condition for coupled atom-light states. Such a transition can be connected with superfluid (coherent) properties of photon-like low branch (LB) polaritons. We discuss the application of metallic cylindrical waveguide for observing predicted effects.Comment: 8 pages, 2 figure

Slow and fast micro-field components in warm and dense hydrogen plasmas

The aim of this work is the investigation of the statistical properties of local electric fields in an ion-electron two component plasmas for coupled conditions. The stochastic fields at a charged or at a neutral point in plasmas involve both slow and fast fluctuation characteristics. The statistical study of these local fields based on a direct time average is done for the first time. For warm and dense plasma conditions, typically $N_{e}\approx 10^{18}cm^{-3}$, $$, well controlled molecular dynamics (MD) simulations of neutral hydrogen, protons and electrons have been carried out. Relying on these \textit{ab initio} MD calculations this work focuses on an analysis of the concepts of statistically independent slow and fast local field components, based on the consideration of a time averaged electric field. Large differences are found between the results of these MD simulations and corresponding standard results based on static screened fields. The effects discussed are of importance for physical phenomena connected with stochastic electric field fluctuations, e.g., for spectral line broadening in dense plasmas.Comment: 4 pages, 4 figures, submitted to Phys. Rev. Let

The Correlation-Based Method for the Movement Compensation in the Analysis of the Results of FRAP Experiments

This paper presents a computational algorithm for the detection and compensation for intracellular movement in the FRAP experiments with focal adhesions in living cells. The developed approach is based on the calculation of correlation coefficient. It was validated on the series of the experimental datasets and shows the successful results in the comparison with other widelyestablished methods

Predicting plant Rubisco kinetics from RbcL sequence data using machine learning

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis, and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubisco enzymes for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes, for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubisco enzymes from C4 or crassulacean acid metabolism (CAM) species, compared with those found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, which could be applied to other enzymes

Proceedings of the Scientific-Practical Conference "Research and Development - 2016"

This open access book relates to the III Annual Conference hosted by the Russian Federal Ministry of Education and Science in December 2016. This event has summarized, analyzed and discussed the interim results, academic outputs and scientific achievements of the Russian Federal Targeted Programme for Research and Development in priority areas of development of the Russian Scientific and Technological Complex for 2014-2020. It contains 75 selected papers from 6 areas considered priority by the Federal programme: computer science, ecology & environment sciences; energy and energy efficiency; life sciences; nanoscience & nanotechnology; and transport & communications. The chapters report the results of the 3-years research projects supported by the Programme and finalized in 2016