INVERSE PROBLEMS OF SOIL BIOKINETICS

This work represents the materials of the report prepared at the suggestion of N. S. Panikov in 19851986, when the author was a third-year student at the Faculty of Soil Science, M.V. Lomonosov Moscow State University. The report contains definitions of direct and inverse problems. A classification of inverse problems and several examples of such problems encountered in soil science and biological kinetics are given. The question of the ill-posed inverse problems is touched, and the main methods of their solution are briefly listed. The problem of identifying a gas source in a soil column by the layer-by-layer balance method (based on measurements of the dynamics of the concentration field) is considered in detail. This task is shown as a computer program, and for others, useful links to programs published in the literature are given.

Mathematical model of shallow water self-purification process

The paper covers the model of shallow water self-purification processes. The proposed mathematical model of biological kinetics is based on a system of non-stationary convection-diffusion-reaction equations with nonlinear terms, taking into account the water flow movement, gravitational sedimentation of impurities, microturbulent diffusion, and the detritus decomposition as a result of activity the aerobic and anaerobic bacteria. Discretization is performed on the basis of a linear combination of central and Upwind Leapfrog difference schemes, which makes it possible to increase the solution accuracy of biological kinetics problem at large values of the grid Péclet number (Peh > 2). To solve high-dimensional SLAEs, a modified alternating-triangular method was used.

Mathematical Modeling of the Phytoplankton Populations Geographic Dynamics for Possible Scenarios of Changes in the Azov Sea Hydrological Regime

Increased influence of abiotic and anthropogenic factors on the ecological state of coastal systems leads to uncontrollable changes in the overall ecosystem. This paper considers the crucial problem of studying the effect of an increase in the water’s salinity in the Azov Sea and the Taganrog Bay on hydrobiological processes. The main aim of the research is the diagnostic and predictive modeling of the geographic dynamics of the general phytoplankton populations. A mathematical model that describes the dynamics of three types of phytoplankton is proposed, considering the influence of salinity and nutrients on algae development. Discretization is carried out based on a linear combination of Upwind Leapfrog difference schemes and a central difference scheme, which makes it possible to increase the accuracy of solving the biological kinetics problem at large values of the grid Péclet number (Peh > 2). A software package has been developed that implements interrelated models of hydrodynamics and biogeochemical cycles. A modified alternating-triangular method was used to solve large-dimensional systems of linear algebraic equations (SLAE). Based on the scenario approach, several numerical experiments were carried out to simulate the dynamics of the main species of phytoplankton populations at different levels of water salinity in coastal systems. It is shown that with an increase in the salinity of waters, the habitats of phytoplankton populations shift, and marine species invasively replace freshwater species of algae.

The Dynamics of Subunit Rotation in a Eukaryotic Ribosome

Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ∼1 MDa) undergoes spontaneous and reversible rotation events (∼8∘). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.

The dynamics of subunit rotation in a eukaryotic ribosome

Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ~1MDa) undergoes spontaneous and reversible rotations (~ 8°). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.

Computational aspects of mathematical modeling of the shallow water hydrobiological processes

Статья посвящена изучению нелинейных эффектов в динамике популяции промысловой рыбы пиленгас Азовского моря при низкой и высокой ее численности с учетом эффекта Олли, конкуренции за ресурсы, таксиса, вылова, пространственного распределения биогенных веществ и детрита на основе многовидовой модели взаимодействия планктона и рыб. Дискретный аналог разработанной модельной задачи водной экологии, входящей в состав программного комплекса, получен на основе схем второго порядка точности с учетом частичной заполненности расчетных ячеек. Возникающая в процессе дискретизации система сеточных уравнений большой размерности была решена на основе модифицированного попеременно-треугольного метода, имеющего наибольшую скорость сходимости при условии асимптотической устойчивости разностных схем для параболических уравнений, эффективность которого была улучшена на основе уточненных спектральных оценок. Разработка эффективных параллельных алгоритмов численной реализации поставленной задачи биологической кинетики, ориентированных на многопроцессорную вычислительную систему (МВС) и графический ускоритель NVIDIA Tesla K80 с модификацией формата хранения данных, позволила анализировать процессы воспроизводства популяций биогидроценоза в режиме реального и ускоренного времени. Paper covers the research of nonlinear effects in population dynamics of the pelengas commercial fish of the Azov Sea taking into account the Allee effect, competition for resources, taxis, catching, spatial distribution of biogenic matter and detritus based on a multi-species model of plankton and fish interaction. Discrete analogue of developed model problem of water ecology, included in a software complex, were calculated using schemes of second order of accuracy taking into account the partial filling of computational cells. The system of grid equations of large dimension, arising at discretization, has been solved on the basis of adaptive modified alternately triangual variational method. Effective parallel algorithms were developed for numerical implementation of biological kinetics problem and oriented on multiprocessor computer system and NVIDIA Tesla K80 graphics accelerator with the data storage format modification. Due to it, the reproduction processes of biogeocenose populations have been analyzed in real and accelerated time.

Multichannel satellite image application for water surface objects identification

The paper is devoted to the analysis of methods of adoption of satellite observation data in order to identify the required information used in the development and verification of mathematical models of hydrodynamics and biological kinetics of shallow water reservoirs. For the information accumulation, we consider the use of remote sensing data. The aim of the paper is to identify the best implementation method for software tools in order to improve the quality of assimilation of date of satellite sensing of the Earth relating to hydrobiological processes in a shallow water reservoir.