Dynamic model for a magnetorheological damper

A lumped mass thermo-mechanical model for the dynamics of a damper filled with a magnetorheological fluid is described, analyzed, and numerically simulated. The model includes friction and temperature effects, and consists of a differential inclusion for the piston displacements coupled with the energy balance equation for the temperature. The fluid viscosity is assumed to be a function the temperature and electrical current, which in practice may be used as the control variable. Numerical simulations of the system behavior are presented. In particular, the simulations of an initial impact show how the subsequent oscillations can be effectively damped.     

提高水分子流出纳米碳管速度的特殊水分子偶极排布研究

使用分子动力学的方法,研究了水分子进出狭窄碳纳米管的过程．发现管口处水分子的偶极垂直于碳管时容易流出碳管．根据碳管中与之相邻的水分子的偶极方向可以把这种特殊构型分为2类．虽然,这2类特殊结构的出现概率非常小,但是它们对净流过碳管水分子的贡献与其它结构的贡献基本相同．这2种偶极排布中水分子比较接近管壁、远离Lennard-Jones势的平衡位置,导致这2种偶极排布中水分子能量升高,处于相对不稳定的状态,容易流出碳管．这个发现表明可以通过调控碳纳米管内的水分偶极方向控制管内的水分子流动．     

SBA splitting for approximation of invariants in time-dependent Hamiltonian systems

Most physical phenomena are described by time-dependent Hamiltonian systems with qualitative features that should be preserved by numerical integrators used for approximating their dynamics. The initial energy of the system together with the energy added or subtracted by the outside forces, represent a conserved quantity of the motion. For a class of time-dependent Hamiltonian systems [8] this invariant can be defined by means of an auxiliary function whose dynamics has to be integrated simultaneously with the system’s equations. We propose splitting procedures featured by a SB³A property that allows to construct composition methods with a reduced number of determining order equations and to provide the same high accuracy for both the dynamics and the preservation of the invariant quantity.     

Approximation of periodic solutions for a dissipative hyperbolic equation

This paper studies the numerical approximation of periodic solutions for an exponentially stable linear hyperbolic equation in the presence of a periodic external force $f$ . These approximations are obtained by combining a fixed point algorithm with the Galerkin method. It is known that the energy of the usual discrete models does not decay uniformly with respect to the mesh size. Our aim is to analyze this phenomenon’s consequences on the convergence of the approximation method and its error estimates. We prove that, under appropriate regularity assumptions on $f$ , the approximation method is always convergent. However, our error estimates show that the convergence’s properties are improved if a numerically vanishing viscosity is added to the system. The same is true if the nonhomogeneous term $f$ is monochromatic. To illustrate our theoretical results we present several numerical simulations with finite element approximations of the wave equation in one or two dimensional domains and with different forcing terms.     

Bifurcations and chaos control in a discrete-time predator-prey system of Leslie type

We investigate the dynamics of a discrete-time predator-prey system of Leslie type. We show algebraically that the system passes through a flip bifurcation and a Neimark-Sacker bifurcation in the interior of $\R^{2}_+$ using center manifold theorem and bifurcation theory. Numerical simulations are implimented not only to validate theoretical analysis but also exhibits chaotic behaviors, including phase portraits, period-11 orbits, invariant closed circle, and attracting chaotic sets. Furthermore, we compute Lyapunov exponents and fractal dimension numerically to justify the chaotic behaviors of the system. Finally, a state feedback control method is applied to stabilize the chaotic orbits at an unstable fixed point.     

A mathematical investigation of the Car-Parrinello method

The Car-Parrinello method for ab-initio molecular dynamics avoids the explicit minimization of energy functionals given by functional density theory in the context of the quantum adiabatic approximation (time-dependent Born-Oppenheimer approximation). Instead, it introduces a fictitious classical dynamics for the electronic orbitals. For many realistic systems this concept allowed first-principle computer simulations for the first time. In this paper we study the quantitative influence of the involved parameter , the fictitious electronic mass of the method. In particular, we prove by use of a carefully chosen two-time-scale asymptotics that the deviation of the Car-Parrinello method from the adiabatic model is of order – provided one starts in the ground state of the electronic system and the electronic excitation spectrum satisfies a certain non-degeneracy condition. Analyzing a two-level model problem we prove that our result cannot be improved in general. Received June 14, 1996     

Application of molecular dynamics computer simulations in the design of a minimal self‐replicating molecular machine

It is commonly agreed that a chemical assembly of molecules can be considered alive if it can ingest resources and convert them into building blocks; has the ability to grow and self‐reproduce; and can evolve. In the design proposed by Rasmussen and Chen (Science 2004, 303, 963) the assembly or protocell could be as simple as a small micellar surfactant aggregate acting as a container, anchoring an informational molecule to its exterior and incorporating a metabolism within the oily interior. We present several examples of modeling such a system with molecular dynamics computer simulations. © 2008 Wiley Periodicals, Inc. Complexity, 2008.     

A good approximation of modulated amplitude waves in Bose–Einstein condensates

In this paper, we present a perturbation method that utilizes Hamiltonian perturbation theory and averaging to analyze spatio-temporal structures in Gross–Pitaevskii equations and thereby investigate the dynamics of modulated amplitude waves (MAWs) in quasi-one-dimensional Bose–Einstein condensates with mean-field interactions. A good approximation for MAWs is obtained. We also explore dynamics of BECs with the nonresonant external potentials and scatter lengths varying periodically in detail using Hamiltonian perturbation theory and numerical simulations.     

The drift of spirals under competitive illumination in an excitable medium

We study numerically the resonant drift of spirals induced by periodic illuminations in excitable media for the Oregonator model. Differential phase illumination of a competitive system with an interface causes interesting spiral drift behavior which can be related to the phase difference. It is found that the drift directions and velocities have been controlled by changing their phase differences, and the spiral has been forbidden to drift back to the initial region due to the interface. Furthermore, the simulation result seems to be reliable as it is also consistent perfectly with the theoretical analysis based on the weak deformation approximation.     

Polynomial Conservation Laws in Quantum Systems

We consider systems with a finite number of degrees of freedom and potential energy that is a finite sum of exponentials with purely imaginary or real exponents. Such systems include the generalized Toda chains and systems with a toric configuration space. We consider the problem of describing all the quantum conservation laws, i.e., the differential operators that are polynomial in the derivatives and commute with the Hamiltonian operator. We prove that in the case where the potential energy spectrum is invariant under reflection with respect to the origin, such nontrivial operators exist only if the system under consideration decomposes into a direct sum of decoupled subsystems. In the general case (without the spectrum symmetry assumption), we prove that the existence of a complete set of independent conservation laws implies the complete integrability of the corresponding classical system.     

Protein dynamics: Complex by itself

Biological functions are intimately rooted in biopolymer dynamics. It is commonly accepted that proteins can be considered as complex systems, but the origin of such complexity is still not fully understood. Moreover, it is still not really clear if proteins are true complex systems or complicated ones. Here, molecular dynamics simulations on a two helix bundle protein have been performed, and protein trajectories have been analyzed by using correlation functions in the frequency domain. We show that even a simple protein exhibits the hallmarks of complex systems. Moreover, the molecular bases of this complex behavior are possessed completely by the protein itself, because such complexity emerges without considering the solvent explicitly. © 2012 Wiley Periodicals, Inc. Complexity, 2012     

Foliations of isonergy surfaces and singularities of curves

It is well known that changes in the Liouville foliations of the isoenergy surfaces of an integrable system imply that the bifurcation set has singularities at the corresponding energy level.We formulate certain genericity assumptions for two degrees of freedom integrable systems and we prove the opposite statement: the essential critical points of the bifurcation set appear only if the Liouville foliations of the isoenergy surfaces change at the corresponding energy levels. Along the proof, we give full classification of the structure of the isoenergy surfaces near the critical set under our genericity assumptions and we give their complete list using Fomenko graphs. This may be viewed as a step towards completing the Smale program for relating the energy surfaces foliation structure to singularities of the momentum mappings for non-degenerate integrable two degrees of freedom systems.      

Hydrodynamic limit for the velocity-flip model

We study the diffusive scaling limit for a chain of N$N$ coupled oscillators. In order to provide the system with good ergodic properties, we perturb the Hamiltonian dynamics with random flips of velocities, so that the energy is locally conserved. We derive the hydrodynamic equations by estimating the relative entropy with respect to the local equilibrium state, modified by a correction term.     

Continuous-time limit of repeated interactions for a system in a confining potential

We study the continuous-time limit of a class of Markov chains coming from the evolution of classical open systems undergoing repeated interactions. This repeated interaction model has been initially developed for dissipative quantum systems in Attal and Pautrat (2006) and was recently set up for the first time in Deschamps (2012) for classical dynamics. It was particularly shown in the latter that this scheme furnishes a new kind of Markovian evolutions based on Hamilton’s equations of motion. The system is also proved to evolve in the continuous-time limit with a stochastic differential equation. We here extend the convergence of the evolution of the system to more general dynamics, that is, to more general Hamiltonians and probability measures in the definition of the model. We also present a natural way to directly renormalize the initial Hamiltonian in order to obtain the relevant process in a study of the continuous-time limit. Then, even if Hamilton’s equations have no explicit solution in general, we obtain some bounds on the dynamics allowing us to prove the convergence in law of the Markov chain on the system to the solution of a stochastic differential equation, via the infinitesimal generators.     

Feedback Integrators

A new method is proposed to numerically integrate a dynamical system on a manifold such that the trajectory stably remains on the manifold and preserves the first integrals of the system. The idea is that given an initial point in the manifold we extend the dynamics from the manifold to its ambient Euclidean space and then modify the dynamics outside the intersection of the manifold and the level sets of the first integrals containing the initial point such that the intersection becomes a unique local attractor of the resultant dynamics. While the modified dynamics theoretically produces the same trajectory as the original dynamics, it yields a numerical trajectory that stably remains on the manifold and preserves the first integrals. The big merit of our method is that the modified dynamics can be integrated with any ordinary numerical integrator such as Euler or Runge–Kutta. We illustrate this method by applying it to three famous problems: the free rigid body, the Kepler problem and a perturbed Kepler problem with rotational symmetry. We also carry out simulation studies to demonstrate the excellence of our method and make comparisons with the standard projection method, a splitting method and Störmer–Verlet schemes.     

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.     

Adiabatic Invariance and Applications: From Molecular Dynamics to Numerical Weather Prediction

A wide class of Hamiltonian systems exhibit a mixture of slow motion with superimposed fast oscillations. Under the assumption of scale separation, these systems can be investigated using the principle of adiabatic invariance. In this paper, we start with a review of some of the main theoretical and numerical findings. We then briefly summarize a few important implications for molecular dynamics (MD) before we provide a more extensive discussion of numerical weather prediction (NWP). In particular, the conservative Hamiltonian particle-mesh (HPM) method is extended to Euler's equation and the fundamental concepts of geostrophic and hydrostatic balance are illustrated on the level of fluid blobs. We also demonstrate numerically that symplectic time-stepping methods are able to maintain hydrostatic balance to high accuracy.     

Stochastic recursive inclusions with non-additive iterate-dependent Markov noise

In this paper we study the asymptotic behaviour of stochastic approximation schemes with set-valued drift function and non-additive iterate-dependent Markov noise. We show that a linearly interpolated trajectory of such a recursion is an asymptotic pseudotrajectory for the flow of a limiting differential inclusion obtained by averaging the set-valued drift function of the recursion w.r.t. the stationary distributions of the Markov noise. The limit set theorem by Benaim is then used to characterize the limit sets of the recursion in terms of the dynamics of the limiting differential inclusion. We then state two variants of the Markov noise assumption under which the analysis of the recursion is similar to the one presented in this paper. Scenarios where our recursion naturally appears are presented as applications. These include controlled stochastic approximation, subgradient descent, approximate drift problem and analysis of discontinuous dynamics all in the presence of non-additive iterate-dependent Markov noise.     

Global convergence of the Euler‐Poisson system for ion dynamics

We consider smooth solutions of the Euler‐Poisson system for ion dynamics in which the electron density is replaced by a Boltzmann relation. The system arises in the modeling of plasmas, where appear two small parameters, the relaxation time and the Debye length. When the initial data are sufficiently close to constant equilibrium states, we prove the convergence of the system for all time, as each of the parameters goes to zero. The limit systems are drift‐diffusion equations and compressible Euler equations. The proof is based on uniform energy estimates and compactness arguments.