The advent of ab initio simulations of dense plasmas

We present the story of full three-dimensional ab initio simulation techniques of dense plasmas based on the Kohn–Sham realization of the density functional theory, starting from early attempts using the Car–Parrinello method to the most recent approaches based on density matrix. We recall the decisive role played by two experiments, one on the Nova laser and the other at a much smaller scale, with pulsed electrical discharges. We emphasize that the essential roles of the Physics of Non-Ideal Plasmas (PNP) and Strongly Coupled Coulomb Systems (SCCS) conference series were most results, and simulation tools were presented and discussed under the benevolent presence of Vladimir Fortov.     

Numerical comparisons of time–space iterative method and spatial iterative methods for the stationary Navier–Stokes equations

This paper makes some numerical comparisons of time–space iterative method and spatial iterative methods for solving the stationary Navier–Stokes equations. The time–space iterative method consists in solving the nonstationary Stokes equations based on the time–space discretization by the Euler implicit/explicit scheme under a weak uniqueness condition (A2). The spatial iterative methods consist in solving the stationary Stokes scheme, Newton scheme, Oseen scheme based on the spatial discretization under some strong uniqueness assumptions. We compare the stability and convergence conditions of the time–space iterative method and the spatial iterative methods. Moreover, the numerical tests show that the time–space iterative method is the more simple than the spatial iterative methods for solving the stationary Navier–Stokes problem. Furthermore, the time–space iterative method can solve the stationary Navier–Stokes equations with some small viscosity and the spatial iterative methods can only solve the stationary Navier–Stokes equations with some large viscosities.     

从头计算分子动力学

Ｃａｒ、Ｐａｒｒｉｎｅｌｏ首次提出的从头计算分子动力学方法有机地结合了密度泛函理论和分子动力学技术,是目前计算机模拟实验中最先进最重要的方法之一。本文简要地阐述了从头计算分子动力学方法的原理和具体实现,以及近年来这一方法的发展和重要应用。     

The method of local fields: A bridge between molecular modelling and dielectric theory

At the nanoscale, the charge distribution in a cluster of several atoms or molecules can be calculated ab initio, i.e. without free parameters. Molecular modelling is limited to a relatively small number of atoms compared to macroscopic materials with myriads of atoms. On the other hand, dielectric and ferroelectric properties of macroscopic matter are described by classical theory using mean-field approximations, e. g. the formula of Clausius–Mossotti for dielectrics and the Landau–Ginzburg–Devonshire theory or rather the molecular field theory by Weiss for ferroelectrics. In the context of multiscale simulations we present a microscopic model for dielectrics and ferroelectrics consisting of discrete atoms and / or dipoles. Parameters calculated from molecular modelling can be used here as input to our simulations in order to calculate bigger systems now. All electrostatic interactions are considered and the electrodes are taken into account using the method of images. Based on thermally activated processes, permanent dipoles fluctuate in double well potentials according to the Boltzmann statistics. Neutral atoms are modelled by induced dipoles having dipole moments proportional to the locally prevailing field. The numerical calculations are based on deterministic local field computations and on weighted probabilistic dynamic Monte Carlo steps.     

Free energy computations by minimization of Kullback–Leibler divergence: An efficient adaptive biasing potential method for sparse representations

The present paper proposes an adaptive biasing potential technique for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and estimating the free energy function, under the same objective of minimizing the Kullback–Leibler divergence between appropriately selected densities. It offers rigorous convergence diagnostics even though history dependent, non-Markovian dynamics are employed. It makes use of a greedy optimization scheme in order to obtain sparse representations of the free energy function which can be particularly useful in multidimensional cases. It employs embarrassingly parallelizable sampling schemes that are based on adaptive Sequential Monte Carlo and can be readily coupled with legacy molecular dynamics simulators. The sequential nature of the learning and sampling scheme enables the efficient calculation of free energy functions parametrized by the temperature. The characteristics and capabilities of the proposed method are demonstrated in three numerical examples.     

"Learn on the fly": a hybrid classical and quantum-mechanical molecular dynamics simulation

We describe and test a novel molecular dynamics method which combines quantum-mechanical embedding and classical force model optimization into a unified scheme free of the boundary region, and the transferability problems which these techniques, taken separately, involve. The scheme is based on the idea of augmenting a unique, simple parametrized force model by incorporating in it, at run time, the quantum-mechanical information necessary to ensure accurate trajectories. The scheme is tested on a number of silicon systems composed of up to approximately 200 000 atoms.     

Study of the stable structures of Ga6As6 cluster using FP-LMTO MD method

We have investigated the structures and energies of a Ga₆As₆ cluster using full-potential linear-muffin-tin-orbital molecular-dynamics calculations. 9 stable structures were obtained for a Ga₆As₆ cluster, including the structure, a cube with two capped Ga–As pairs considered by Yi (Chem. Phys. Lett. 325 (2000) 269), who used the Car–Parrinello method based on the pseudopotential method and the local density functional formalism. However, the ground state we obtained is a distorted structure of a bicapped pentaprism, the energy of which is lower than that of Yi. Furthermore, we found the structure a1 presented semiconductor-like properties through the calculation of the density of states.     

Influence of Structural Defects on Martensitic Transformations in Systems with Low Elastic Moduli

We have developed a computational scheme within the Parrinello and Rahman molecular dynamics method allowing changes in the volume and shape of the model block. The scheme enables us to study the considerable structural rearrangement of the system in response to an arbitrary stress tensor. The effects of the type, symmetry, and interaction of regularly spaced point-defect complexes and stacking faults on the lattice stability and martensitic-transformation realization in bcc and B2-structures are investigated. It is shown that the defects can both stabilize the parent structure and contribute to its instability and development of the transformation by the shear mechanism. The actual scenario will depend on the defect type and symmetry. It is found that in the premartensite state, where the system approaches its stability limit, the interaction of strain fields occurring in the vicinity of defects may affect the choice of possible martensite-transition pathways.     

Modeling hydrogen exchange of proteins by a multiscale method

We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments. By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm, we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations. We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy. These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.     

Nonlocal excitonic–mechanical interaction in a nanosystem

The dynamics of a nanoparticle during its dipole interaction with an excitonic excitation in an extended quasi-one-dimensional polarizable medium is investigated. Bundles of J-aggregates of dye molecules are considered as an example of the latter. The nonlocal excitonic–mechanical interaction between the field of an amplifying or absorbing nanoparticle and excitons in a bundle has been simulated numerically. It has been found that the interaction between the field of the induced nanoparticle dipole and the fields of the molecular dipoles in an aggregate can lead to a change in the particle trajectory and excitonic pulse shape. The possibility of controlling the nanoparticle by excitonic pulses and the reverse effect of the nanoparticle field on the dynamics of excitons due to the nonlocal excitonic–mechanical interaction has been demonstrated.     

A novel approach to the simulation of nitroxide spin label EPR spectra from a single truncated dynamical trajectory

A simple effective method for calculation of EPR spectra from a single truncated dynamical trajectory of spin probe orientations is reported. It is shown that an accurate simulation can be achieved from the small initial fraction of a dynamical trajectory until the point when the autocorrelation function of re-orientational motion of spin label has relaxed. This substantially reduces the amount of time for spectra simulation compared to previous approaches, which require multiple full length trajectories (normally of several microseconds) to achieve the desired resolution of EPR spectra. Our method is applicable to trajectories generated from both Brownian dynamics and molecular dynamics (MD) calculations. Simulations of EPR spectra from Brownian dynamical trajectories under a variety of motional conditions including bi-modal dynamics with different hopping rates between the modes are compared to those performed by conventional method. Since the relatively short timescales of spin label motions are realistically accessible by modern MD computational methods, our approach, for the first time, opens the prospect of the simulation of EPR spectra entirely from MD trajectories of real proteins structures.     

Oxygen impact on quantum confinement effect for silicon clusters in different size regimes: ab initio investigations

The phenomena where the parameter like optical gap, HOMO-LUMO gap etc of a cluster will behave like a monotonic function with respect to its size is called quantum confinement effect. Here we are dealing with clusters having number of silicon atoms as 10, 16, 19, 20, 35, 54 and 78 which are representatives of different size regime clusters. For each clusters we have experimented with a number of isomers and the results we are showing are only of the stable most isomers. Then for each clusters we are capping them with oxygen atoms and calculating their optical response using DFT based calculations. We also calculate their HOMO-LUMO gap with and without oxygen atoms. The main essence of this work is mainly revolving around the variation of optical gap as well as the HOMO-LUMO gap for all the clusters with respect to their size and also whether oxygen insertion can induce any changes in quantum confinement effect. Also for Si₂₀, Si₁₉, Si₁₆ and Si₁₀ we have calculating the optical spectra with a variation of inserted oxygen on the surface of those clusters. All the calculation are performed using Vienna ab initio simulation package (VASP) and Car Parrinello molecular dynamics (CPMD) for geometry optimization. The optical spectra of the clusters are performed by real space PARSEC code and time dependent density functional theory implemented RGWBS code which takes into account the many body effects using GW and BSE equations.     

基于LU-SGS的非结构弹簧网格迭代算法

针对运动间断拟合中需频繁更新网格点位置的特点,提出一种基于LU-SGS(lower-upper symmetricGauss-Seidel)迭代方法的非结构弹簧网格运动算法.根据弹簧网格原理构建与网格拓扑关系相对应的稀疏系数矩阵,将LU-SGS思想成功引入动网格迭代算法,并辅以合理的网格运动管理策略,实现动网格的快速迭代.研究表明,在非结构网格下,LU-SGS算法可以满足运动间断拟合的需求,在流场隐式时间推进时,仍能保证获得稳定解;与传统的SOR方法相比,计算时耗减少20%以上.     

Time-reversible Born-Oppenheimer molecular dynamics

We present a time-reversible Born-Oppenheimer molecular dynamics scheme, based on self-consistent Hartree-Fock or density functional theory, where both the nuclear and the electronic degrees of freedom are propagated in time. We show how a time-reversible adiabatic propagation of the electronic degrees of freedom is possible despite the nonlinearity and incompleteness of the self-consistent field procedure. With a time-reversible lossless propagation the simulated dynamics is stabilized with respect to a systematic long-term energy drift and the number of self-consistency cycles can be kept low thanks to a good initial guess given from the electronic propagation. The proposed molecular dynamics scheme therefore combines a low computational cost with a physically correct time-reversible representation, which preserves a detailed balance between propagation forwards and backwards in time.     

A high-order spectral deferred correction strategy for low Mach number flow with complex chemistry

We present a fourth-order finite-volume algorithm in space and time for low Mach number reacting flow with detailed kinetics and transport. Our temporal integration scheme is based on a Multi-Implicit Spectral Deferred Correction (MISDC) strategy that iteratively couples advection, diffusion, and reactions evolving subject to a constraint. Our new approach overcomes a stability limitation of our previous second-order method encountered when trying to incorporate higher-order polynomial representations of the solution in time to increase accuracy. We have developed a new iterative scheme that naturally fits within our MISDC framework and allows us to conserve mass and energy while simultaneously satisfying the equation of state. We analyse the conditions for which the iterative schemes are guaranteed to converge to the fixed point solution. We present numerical examples illustrating the performance of the new method on premixed hydrogen, methane, and dimethyl ether flames.     

Protein folding kinetics and thermodynamics from atomistic simulations

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/- 0.4 micros, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.     

Action-derived molecular dynamics in the study of rare events

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.     

Engineering multipartite steady entanglement of distant atoms via dissipation

We propose a scheme for generating an entangled state for three atoms trapped in separate optical cavities that are coupled to each other through two optical fibers based on coherent driving and dissipation, which are induced by the classical fields and the decay of non-local bosonic modes, respectively. In our scheme, the interaction time need not be controlled strictly in the overall dynamics process, and the cavity field decay can be changed into a vital resource. The numerical simulation shows that the fidelity of the target state is insensitive to atomic spontaneous emission, and our scheme is good enough to generate the W state of distant atoms with a high fidelity and purity. In addition, the present scheme can also be generalized to prepare the N-partite W state of distant atoms.     

Large Scale Dynamics of the Persistent Turning Walker Model of Fish Behavior

This paper considers a new model of individual displacement, based on fish motion, the so-called Persistent Turning Walker (PTW) model, which involves an Ornstein-Uhlenbeck process on the curvature of the particle trajectory. The goal is to show that its large time and space scale dynamics is of diffusive type, and to provide an analytic expression of the diffusion coefficient. Two methods are investigated. In the first one, we compute the large time asymptotics of the variance of the individual stochastic trajectories. The second method is based on a diffusion approximation of the kinetic formulation of these stochastic trajectories. The kinetic model is a Fokker-Planck type equation posed in an extended phase-space involving the curvature among the kinetic variables. We show that both methods lead to the same value of the diffusion constant. We present some numerical simulations to illustrate the theoretical results.