An iterative langevin solution for turbulent dispersion in the atmosphere

In this work we present an alternative hybrid method to solve the Langevin equation and we apply it to simulate air pollution dispersion in inhomogeneous turbulence conditions. The method solves the Langevin equation, in semi-analytical manner, by the method of successive approximations or Picard's Iterative Method. Solutions for Gaussian and non-Gaussian turbulence conditions, considering Gaussian, bi-Gaussian and Gram–Charlier probability density functions are obtained. The models are applied to study the pollutant dispersion in all atmospheric stability and in low-wind speed condition. The proposed approach is evaluated through the comparison with experimental data and results from other different dispersion models. A statistical analysis reveals that the model simulates very well the experimental data and presents results comparable or even better than ones obtained by the other models.     

The heterogeneous multiscale method as a framework for coupling the finite element method and molecular dynamics

Hierarchical two-scale methods are computationally very powerful as there is no direct coupling between the macro- and microscale. Such schemes develop first a microscale model under macroscopic constraints, then the macroscopic constitutive laws are found by averaging over the microscale. The heterogeneous multiscale method (HMM) is a general top-down approach for the design of multiscale algorithms. While this method is mainly used for concurrent coupling schemes in the literature, the proposed methodology also applies to a hierarchical coupling. This contribution discusses a hierarchical two-scale setting based on the heterogeneous multi-scale method for quasi-static problems: the macroscale is treated by continuum mechanics and the finite element method and the microscale is treated by statistical mechanics and molecular dynamics. Our investigation focuses on an optimised coupling of solvers on the macro- and microscale which yields a significant decrease in computational time with no associated loss in accuracy. In particular, the number of time steps used for the molecular dynamics simulation is adjusted at each iteration of the macroscopic solver. A numerical example demonstrates the performance of the model. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

On the stability of boundary conditions for molecular dynamics

We study the stability of boundary conditions for molecular dynamics simulations. A general stability criterion is established. We first consider a one-dimensional model with nearest neighbor interaction and multiple-neighbor interactions. We then generalize the results to more realistic models in 3D with nonlinear atomic interaction.     

Tests for a given linear structure of the mean direction of the langevin distribution

This paper deals with Watson statistic T _w and likelihood ratio (LR) statistic T _l for testing hypothesis H _0s: V (a given s-dimensional subspace) based on a sample of size n from a p-variate Langevin distribution M _p(, ). Asymptotic expansions of the null and non-null distributions of T _w and T _l are obtained when n is large. Asymptotic expressions of those powers are also obtained. It is shown that the powers of them are coincident up to the order n ^-1 when is unknown.     

A molecular dynamics model for symplectic intergrators

Mechanical systems in the very large scale like in celestial mechanics or in the very small scale like in the molecular dynamics can be modelled without dissipation. The resulting Hamiltonian systems possess conservation properties, which are characterized with the term symplecticness, Numerical integration schemes should preserve the symplecticness. Different methods are introduced and their performance is studied for constant and variable step size. As test examples two systems from molecular dynamics are introduced.     

Application of the string method to compute minimum energy paths for a chain of bi-stable elements using the finite element method and molecular dynamics

Activated processes are frequently found in solid state mechanics. The energy landscape of such processes show a non-convex behaviour, and therefore the computation of energy barriers between two stable minima is of importance. Such barriers are revealed by computing minimum energy paths. The string method is a simple and efficient algorithm to move curves over an energy landscape and to identify minimum energy paths. A hierarchical two-scale model recently introduced to the literature (molecular dynamics coupled with the finite element method) is used in this paper to investigate the string method in a model phase transition in a copper single crystal. To do so, bi-stable elements are constructed and the energetic behaviour of a two-elements chain is investigated. We identify successfully the minimum energy path between two local stable minima of the chain and demonstrate thereby the performance of the string method applied to a complex multiscale model. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

A test problem for molecular dynamics integrators

We derive a test problem for evaluating the ability of time-steppingmethods to preserve the statistical properties of systems inmolecular dynamics. We consider a family of deterministic systemsconsisting of a finite number of particles interacting on acompact interval. The particles are given random initial conditionsand interact through instantaneous energy- and momentum-conservingcollisions. As the number of particles, the particle density,and the mean particle speed go to infinity, the trajectory ofa tracer particle is shown to converge to a stationary Gaussianstochastic process. We approximate this system by one describedby a system of ordinary differential equations and provide numericalevidence that it converges to the same stochastic process. Wesimulate the latter system with a variety of numerical integrators,including the symplectic Euler method, a fourth-order Runge-Kuttamethod, and an energyconserving step-and-project method. Weassess the methods' ability to recapture the system's limitingstatistics and observe that symplectic Euler performs significantlybetter than the others for comparable computational expense.     

Analysis of temperature time-series: Embedding dynamics into the MDS method

Global warming and the associated climate changes are being the subject of intensive research due to their major impact on social, economic and health aspects of the human life. Surface temperature time-series characterise Earth as a slow dynamics spatiotemporal system, evidencing long memory behaviour, typical of fractional order systems. Such phenomena are difficult to model and analyse, demanding for alternative approaches. This paper studies the complex correlations between global temperature time-series using the Multidimensional scaling (MDS) approach. MDS provides a graphical representation of the pattern of climatic similarities between regions around the globe. The similarities are quantified through two mathematical indices that correlate the monthly average temperatures observed in meteorological stations, over a given period of time. Furthermore, time dynamics is analysed by performing the MDS analysis over slices sampling the time series. MDS generates maps describing the stations’ locus in the perspective that, if they are perceived to be similar to each other, then they are placed on the map forming clusters. We show that MDS provides an intuitive and useful visual representation of the complex relationships that are present among temperature time-series, which are not perceived on traditional geographic maps. Moreover, MDS avoids sensitivity to the irregular distribution density of the meteorological stations.     

Parallel constrained molecular dynamics

A block version of the Shake method for heavy atom simulation in biological systems is presented in this paper. The method solves successively, independent blocks of constraints of small size by a Newton method. This algorithm is implemented in TAKAKAW, an efficient parallel molecular dynamics code. This method has been tested on a small system and on an ionic canal of 67671 atoms. This revised version was published online in June 2006 with corrections to the Cover Date.     

Energy behaviour of the Boris method for charged-particle dynamics

The Boris algorithm is a widely used numerical integrator for the motion of particles in a magnetic field. This article proves near-conservation of energy over very long times in the special cases where the magnetic field is constant or the electric potential is quadratic. When none of these assumptions is satisfied, it is illustrated by numerical examples that the numerical energy can have a linear drift or its error can behave like a random walk. If the system has a rotational symmetry and the magnetic field is constant, then also the momentum is approximately preserved over very long times, but in a spatially varying magnetic field this is generally not satisfied.     

Modified potential energy functions for constrained molecular dynamics

In molecular dynamics the highly oscillatory vibrations in the chemical bonds are often replaced by holonomic constraints that freeze the bond length/angle to its equilibrium value. In some cases this approach can be justified if the force constants of the bond vibrations are sufficiently large. However, for moderate values of the force constant, the constrained system might lead to a dynamical behavior that is too “rigid” compared to the flexible model. To compensate for this effect, the concept of soft constraints was introduced in [7,12,13]. However, its implementation is rather expensive. In this paper, we suggest an alternative approach that modifies the force field instead of the constraint functions. This leads to a more efficient method that avoids the resonance induced instabilities of multiple-time-stepping [5] and the above described effect of standard constrained dynamics. This revised version was published online in June 2006 with corrections to the Cover Date.     

分子动力学模拟中非成键相互作用计算的误差估计

高效的非成键相互作用计算对于分子动力学模拟具有核心意义.本文在一个统一的框架下,综述短程相互作用的截断方法、长程静电相互作用的光滑粒子网格Ewald方法和交错网格Ewald方法的误差估计.与传统的误差估计假设体系均匀且无相关性不同,本文介绍的误差估计可以推广到非均匀和有相关性的体系.本文通过具体例子讨论非均匀性和相关性对误差的本质性影响,以及可能的修正方式,并说明误差估计对于提高非成键相互作用的计算精度和速度有重要作用.本文还展示一个针对光滑粒子网格Ewald方法的实用参数优化方法,使得在保证精度的同时选取计算效率近似最优的参数组合成为可能,改善了传统上参数全凭经验选取的局面.     

Finite-difference method for the system of equations of tide dynamics

For the system of shallow water equations describing the tidal wave propagation, we construct a finite-difference scheme on an unstructured grid. We analyze the properties of the resulting system of equations; in particular, we show that, after the elimination of part of the variables, the matrix of the system becomes an M-matrix.     

Convergence of the contour dynamics method

In this paper the contour dynamics method (CDM) is formulated and applied to the study of a two-dimensional incompressible and inviscid fluid flow. A result concerning the convergence of this method is proved. The foundation of the CDM is based on the study of the dynamic interaction between contours enclosing vortex regions. The idea of the analysis is to show that the CDM can be considered as a vortex filament method. Hence, the convergence for the contour dynamics method is proved by using some results in the theory of the vortex method.     

A numerical method for the dynamics and stability of spiral waves

In this paper we propose a new method of investigating the change of dynamics in reaction-diffusion equations, which is based on approximating the Euclidian norm of state variables along with the introduction of phase space. Our method is simple in implementation and can be applied to study the dynamics of multiple spirals. The method is extended to study the stability of spiral waves by developing an algorithm which is applied to circular and meandering motions.     

Molecular dynamics by the Backward-Euler method

This paper introduces a new computational method for molecular dynamics. The method combines the Backward-Euler scheme for the solution of stiff differential equations with a Langevin-equation approach to the establishment of thermal equilibrium. The method allows the user to choose a cutoff frequency ω_c. Vibrational modes with frequencies below ω_c will be fully excited (receive a mean energy of kT per mode), while modes with frequencies greater than ω_c will be effectively frozen by the method. By setting ω_c = kT/h, one can obtain reasonable agreement with the quantum-mechanical energy distribution among the various modes, despite the classical character of the computation.