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Charge transfer in DNA is simulated by a discrete Holstein model «quantum particle + classical site chain + interaction». Thermostat temperature is taken into account as stochastic force, which acts on classical sites (Langevin equation). Thus dynamics of charge migration along the chain is described by ODE system with stochastic right-hand side. To integrate the system numerically, algorithms of order 1 or 2 are usually applied. We developed «mixed» algorithm having 4th order of accuracy for fast «quantum» variables (note that in quantum subsystem the condition «sum of probabilities of charge being on site is time-constant» must be held), and 2nd order for slow classical variables, which are affecting by stochastic force. The algorithm allows us to calculate trajectories on longer time intervals as compared to standard algorithms. Model calculations of polaron disruption in homogeneous chain caused by temperature fluctuations are given as an example.

The difference scheme for numerical solution of a time-dependant system of two Schrödinger equations with the operator of a spin-orbit interaction for a two-component spinor wave function is offered on the basis of a split method for a time-dependant Schrödinger equations. The computer simulation of the external neutrons’ wave functions evolution with different values of the full moment projection upon internuclear axis and probabilities of their transfer are executed for head-on collisions of ¹⁸O and ⁵⁸Ni nuclei.

We derive a new model of circadian oscillations in Neurospora crassa, which is suitable to analyze both temporal and spatial dynamics of proteins responsible for mechanism of rythms. The model is based on the non-linear interplay between proteins FRQ and WCC which are products of transcription of frequency and white collar genes forming a feedback loop comprised both positive and negative elements. The main component of oscillations mechanism is supposed to be time-delay in biochemical reactions of transcription. We show that the model accounts for various features observed in Neurospora’s experiments such as entrainment by light cycles, phase shift under light pulse, robustness to action of fluctuations and so on. Wave patterns excited during spatial development of the system are studied. It is shown that the wave of synchronization of biorythms arises under basal transcription factors.

Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent require a reliable source of pseudorandom numbers generated at each step of calculation. We present the two main approaches for implementation of pseudorandom number generators on a GPU. In the first approach, inherent in CPU-based calculations, one PRNG produces a stream of pseudorandom numbers in each thread of execution, whereas the second approach builds on the ability of different threads to communicate, thus, sharing random seeds across the entire device. We exemplify the use of these approaches through the development of Ran2, Hybrid Taus, and Lagged Fibonacci algorithms. As an application-based test of randomness, we carry out LD simulations of N independent harmonic oscillators coupled to a stochastic thermostat. This model allows us to assess statistical quality of pseudorandom numbers. We also profile performance of these generators in terms of the computational time, memory usage, and the speedup factor (CPU/GPU time).

Isothermal electroconvection in a dielectric liquid arising in a plane-parallel electrode system due to unipolar injection of charges from the cathode is considered. Spatially periodic rolls structures stability is investigated.

The paper describes the results of computer simulation of time-dependent temperature fields arising in polar dielectrics irradiated by focused electron bunches with average electron energy when analyzing with electron microscopy techniques. The mathematical model was based on solving several-dimensional nonstationary heat conduction equation with use of numerical finite element method. The approximation of thermal source was performed taking into account the estimation of initial electron distribution determined by Monte-Carlo simulation of electron trajectories. The simulation program was designed in Matlab. The geometrical modeling and calculation results demonstrated the main features of model sample heating by electron beam were presented at the given experimental parameters as well as source approximation.

The Goodwin dynamical model under the random external disturbances is considered. A full parametrical analysis for equlibria and cycles of deterministic model is developed. We study probabilistic properties of stochastic attractors using stochastic sensitivity functions technique and numerical methods. A phenomenon of the generation of stochastic business cycles in the zones of stable equilibria is discussed.

The article is dedicated to mathematic modeling of natural water desalination process by method of thermal distillation. The article gives the equations which allow describing the processes of film flowing and boiling of water, steam condensation and vacuum maintenance. The article presents the algorithm of calculation, implemented in MatLab computer mathematic system and Excel electronic tables, and the initial data required for the calculation. The model has been checked for adequacy. The calculation of ten-effect distillation system is given. The results of work can be used in design and optimization of process conditions for distillation systems.

An algorithm of applied problem solving was described to calculate electrical characteristics of electrical field effects in ferroelectrics electron-beam charged. The algorithm was based on implementation of the deterministic model using finite element method as well as taking into account Monte-Carlo simulation results of electron transport. The program application was developed to perform computing experiments.

The paper considers models of platelet thrombus formation in blood plasma flow in a cylindrical vessel, based on the “advection–diffusion” equation and the Fokker–Planck equation. The comparison of the results of calculations based on these models is given. Considered models show qualitatively similar behavior at the initial stage of thrombus formation. А detailed investigation of large clots requires models’ improvement.