Artificial time integration

Many recent algorithmic approaches involve the construction of a differential equation model for computational purposes, typically by introducing an artificial time variable. The actual computational model involves a discretization of the now time-dependent differential system, usually employing forward Euler. The resulting dynamics of such an algorithm is then a discrete dynamics, and it is expected to be “close enough” to the dynamics of the continuous system (which is typically easier to analyze) provided that small – hence many – time steps, or iterations, are taken. Indeed, recent papers in inverse problems and image processing routinely report results requiring thousands of iterations to converge. This makes one wonder if and how the computational modeling process can be improved to better reflect the actual properties sought. In this article we elaborate on several problem instances that illustrate the above observations. Algorithms may often lend themselves to a dual interpretation, in terms of a simply discretized differential equation with artificial time and in terms of a simple optimization algorithm; such a dual interpretation can be advantageous. We show how a broader computational modeling approach may possibly lead to algorithms with improved efficiency. AMS subject classification (2000)  65L05, 65M32, 65N21, 65N22, 65D18     

空位在金刚石近(001)表面扩散的分子动力学模拟

用分子动力学方法模拟了空位在金刚石近(001)表面的扩散过程,研究了温度对空位扩散的影响.结果表明,当温度为1000K左右时,位于近表面第二层上的空位开始向表面运动;当温度在1400—2000K时,空位完全扩散到表面.这与实验结果和其他计算结果符合得很好.同时发现,温度为1400—1800K时,空位的扩散经历了两次迁移运动,其分别对应了均方位移图中的两个极大值.在不施加任何约束的条件下得到了空位的动态扩散路径,空位在金刚石近(001)表面的扩散势垒约为042eV.并探讨了一定温度下空位数目增多及其不同排列 关键词： 金刚石 空位 扩散 分子动力学     

Estimating Invariant Probability Densities for Dynamical Systems

Knowing a probability density (ideally, an invariant density) for the trajectories of a dynamical system allows many significant estimates to be made, from the well-known dynamical invariants such as Lyapunov exponents and mutual information to conditional probabilities which are potentially more suitable for prediction than the single number produced by most predictors. Densities on typical attractors have properties, such as singularity with respect to Lebesgue measure, which make standard density estimators less useful than one would hope. In this paper we present a new method of estimating densities which can smooth in a way that tends to preserve fractal structure down to some level, and that also maintains invariance. We demonstrate with applications to real and artificial data.     

Controlling global stochasticity of Hamiltonian systems by nonlinear perturbation

A method of controlling global stochasticity in Hamiltonian systems by applying nonlinear perturbation is proposed. With the well-known standard map we demonstrate that this control method can convert global stochasticity into regular motion in a wide chaotic region for arbitrary initial condition, in which the control signal remains very weak after a few kicks. The system in which chaos has been controlled approximates to the original Hamiltonian system, and this approach appears robust against small external noise. The mechanism underlying this high control efficiency is intuitively explained. Received 15 January 2002 Published online 6 June 2002     

Numerical simulation of the spatiotemporal evolution of a nanoparticle–plasma system

A one-dimensional nanodusty plasma was modeled by self-consistently coupling a plasma model with nanoparticle growth, charging, and transport models. As nanoparticles grow from subnanometer to tens of nm in diameter, the numerical results predict a rich spatiotemporal structure, including four distinct temporal phases: a charge-limited phase, a charge accumulation phase, an early ion drag phase, and a sheath interaction phase.     

Molecular dynamics simulations on the structures and properties of ε-CL-20-based PBXs ——Primary theoretical studies on HEDM formulation design

Five polymer bonded explosives (PBXs) with the base explosive ε-CL-20 (hexanitrohexaazaisowurtzi- tane), the most important high energy density compound (HEDC), and five polymer binders (Estane 5703, GAP, HTPB, PEG, and F2314) were constructed. Molecular dynamics (MD) method was employed to investigate their binding energies (Ebind), compatibility, safety, mechanical properties, and energetic properties. The information and rules were reported for choosing better binders and guiding formula- tion design of high energy density material (HEDM). According to the calculated binding energies, the ordering of compatibility and stability of the five PBXs was predicted as ε-CL-20/PEG > ε-CL-20/ Estane5703 ≈ε-CL-20/GAP > ε-CL-20/HTPB > ε-CL-20/F2314. By pair correlation function g(r) analyses, hydrogen bonds and vdw are found to be the main interactions between the two components. The elasticity and isotropy of PBXs based ε-CL-20 can be obviously improved more than pure ε-CL-20 crystal. It is not by changing the molecular structures of ε-CL-20 for each binder to affect the sensitivity. The safety and energetic properties of these PBXs are mainly influenced by the thermal capability (C°p) and density (ρ) of binders, respectively.     

Microwave synthesis of magnetic Fe3O4 nanoparticles used as a precursor of nanocomposites and ferrofluids

Methods to synthesize magnetic Fe₃O₄ nanoparticles and to modify the surface of particles are presented in the present investigation. Fe₃O₄ magnetic nanoparticles were prepared by the co-precipitation of Fe³⁺ and Fe²⁺, NH₃·H₂O was used as the precipitating agent to adjust the pH value, and the aging of Fe₃O₄ magnetic nanoparticles was accelerated by microwave (MW) irradiation. The obtained Fe₃O₄ magnetic nanoparticles were characterized by Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM), X-ray powder diffraction (XRD) and vibrating sample magnetometer (VSM). The average size of Fe₃O₄ crystallites was found to be around 8–9 nm. Thereafter, the surface of Fe₃O₄ magnetic nanoparticles was modified by stearic acid. The resultant sample was characterized by FT-IR, scanning electron microscopy (SEM), XRD, lipophilic degree (LD) and sedimentation test. The FT-IR results indicated that a covalent bond was formed by chemical reaction between the hydroxyl groups on the surface of Fe₃O₄ nanoparticles and carboxyl groups of stearic acid, which changed the polarity of Fe₃O₄ nanoparticles. The dispersion of Fe₃O₄ in organic solvent was greatly improved. Effects of reaction time, reaction temperature and concentration of stearic acid on particle surface modification were investigated. In addition, Fe₃O₄/polystyrene (PS) nanocomposite was synthesized by adding surface modified Fe₃O₄ magnetic nanoparticles into styrene monomer, followed by the radical polymerization. The obtained nanocomposite was tested by thermogravimetry (TG), differential scanning calorimetry (DSC) and XRD. Results revealed that the thermal stability of PS was not significantly changed after adding Fe₃O₄ nanoparticles. The Fe₃O₄ magnetic fluid was characterized using UV–vis spectrophotometer, Gouy magnetic balance and laser particle-size analyzer. The testing results showed that the magnetic fluid had excellent stability, and had susceptibility of 4.46×10⁻⁸ and saturated magnetization of 6.56 emu/g. In addition, the mean size d (0.99) of magnetic Fe₃O₄ nanoparticles in the fluid was 36.19 nm.     

Biham–Middleton–Levine model with four-directional traffic

We study the four-directional traffic flow on a two-dimensional lattice. In the case of discrete densities, we assume equal number of vehicles in each lane. Except for the minimum density, the gridlock emerges swiftly. Two kinds of gridlock have been observed. The global gridlock dominates the system when the density is twice the minimum value. At higher densities, the system is pervaded by local gridlocks. We also analyze the time evolution of average speed. In the case of continuous densities, the vehicle numbers vary from lane to lane. The global gridlock is then destroyed by the fluctuations; while the local gridlock can still be observed.     

On existence and regularity of solutions for 2‐D micropolar fluid equations with periodic boundary conditions

In this paper, we prove the existence and uniqueness of a global solution for 2‐D micropolar fluid equation with periodic boundary conditions. Then we restrict ourselves to the autonomous case and show the existence of a global attractor. Copyright © 2006 John Wiley & Sons, Ltd.     

Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed