Structure and relaxations in liquid and amorphous Selenium

We report a molecular dynamics simulation of selenium, described by a three-body interaction. The temperatures T_g and T_c and the structural properties are in agreement with experiment. The mean nearest neighbor coordination number is 2.1. A small pre-peak at about 1 AA^-1 can be explained in terms of void correlations. In the intermediate self-scattering function, i.e. the density fluctuation correlation, classical behavior, alpha- and beta-regimes, is found. We also observe the plateau in the beta-regime below T_g. In a second step, we investigated the heterogeneous and/or homogeneous behavior of the relaxations. At both short and long times the relaxations are homogeneous (or weakly heterogeneous). In the intermediate time scale, lowering the temperature increases the heterogeneity. We connect these different domains to the vibrational (ballistic), beta- and alpha-regimes. We have also shown that the increase in heterogeneity can be understood in terms of relaxations

On the construction of high-order force gradient algorithms for integration of motion in classical and quantum systems

A consequent approach is proposed to construct symplectic force-gradient algorithms of arbitrarily high orders in the time step for precise integration of motion in classical and quantum mechanics simulations. Within this approach the basic algorithms are first derived up to the eighth order by direct decompositions of exponential propagators and further collected using an advanced composition scheme to obtain the algorithms of higher orders. Contrary to the scheme by Chin and Kidwell [Phys. Rev. E 62, 8746 (2000)], where high-order algorithms are introduced by standard iterations of a force-gradient integrator of order four, the present method allows to reduce the total number of expensive force and its gradient evaluations to a minimum. At the same time, the precision of the integration increases significantly, especially with increasing the order of the generated schemes. The algorithms are tested in molecular dynamics and celestial mechanics simulations. It is shown, in particular, that the efficiency of the new fourth-order-based algorithms is better approximately in factors 5 to 1000 for orders 4 to 12, respectively. The results corresponding to sixth- and eighth-order-based composition schemes are also presented up to the sixteenth order. For orders 14 and 16, such highly precise schemes, at considerably smaller computational costs, allow to reduce unphysical deviations in the total energy up in 100 000 times with respect to those of the standard fourth-order-based iteration approach.Comment: 23 pages, 2 figures; submitted to Phys. Rev.

An orbital-free molecular dynamics study of melting in K_20, K_55, K_92, K_142, Rb_55 and Cs_55 clusters

The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behavior of Na_55 and K_55. As the atomic number increases, the height of the specific heat peaks decreases, their width increases, and the melting temperature decreases as in bulk melting, but in a more pronounced way.Comment: LaTeX file. 6 pages with 17 pictures. Final version with minor change

Spontaneous alloying in binary metal microclusters - A molecular dynamics study -

Microcanonical molecular dynamics study of the spontaneous alloying(SA), which is a manifestation of fast atomic diffusion in a nano-sized metal cluster, is done in terms of a simple two dimensional binary Morse model. Important features observed by Yasuda and Mori are well reproduced in our simulation. The temperature dependence and size dependence of the SA phenomena are extensively explored by examining long time dynamics. The dominant role of negative heat of solution in completing the SA is also discussed. We point out that a presence of melting surface induces the diffusion of core atoms even if they are solid-like. In other words, the {\it surface melting} at substantially low temperature plays a key role in attaining the SA.Comment: 15 pages, 12 fgures, Submitted to Phys.Rev.

Dynamical Properties and Plasmon Dispersion of a Weakly Degenerate Correlated One-Component Plasma

Classical Molecular Dynamics (MD) simulations for a one-component plasma (OCP) are presented. Quantum effects are included in the form of the Kelbg potential. Results for the dynamical structure factor are compared with the Vlasov and RPA (random phase approximation) theories. The influence of the coupling parameter $\Gamma$, degeneracy parameter $\rho \Lambda^3$ and the form of the pair interaction on the optical plasmon dispersion is investigated. An improved analytical approximation for the dispersion of Langmuir waves is presented.Comment: 23 pages, includes 7 ps/eps-figures and 2 table

Variational Approach to Molecular Kinetics

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics

Effect of the integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration

Although calculations of free energy using molecular dynamics simulations have gained significant importance in the chemical and biochemical fields, they still remain quite computationally intensive. Furthermore, when using thermodynamic integration, numerical evaluation of the integral of the Hamiltonian with respect to the coupling parameter may introduce unwanted errors in the free energy. In this paper, we compare the performance of two numerical integration techniques-the trapezoidal and Simpson's rules and propose a new method, based on the analytic integration of physically based fitting functions that are able to accurately describe the behavior of the data. We develop and test our methodology by performing detailed studies on two prototype systems, hydrated methane and hydrated methanol, and treat Lennard-Jones and electrostatic contributions separately. We conclude that the widely used trapezoidal rule may introduce systematic errors in the calculation, but these errors are reduced if Simpson's rule is employed, at least for the electrostatic component. Furthermore, by fitting thermodynamic integration data, we are able to obtain precise free energy estimates using significantly fewer data points (5 intermediate states for the electrostatic component and 11 for the Lennard-Jones term), thus significantly decreasing the associated computational cost. Our method and improved protocol were successfully validated by computing the free energy of more complex systems hydration of 2-methylbutanol and of 4-nitrophenol-thus paving the way for widespread use in solvation free energy calculations of drug molecules

Atomic-scale modeling of the deformation of nanocrystalline metals

Nanocrystalline metals, i.e. metals with grain sizes from 5 to 50 nm, display technologically interesting properties, such as dramatically increased hardness, increasing with decreasing grain size. Due to the small grain size, direct atomic-scale simulations of plastic deformation of these materials are possible, as such a polycrystalline system can be modeled with the computational resources available today. We present molecular dynamics simulations of nanocrystalline copper with grain sizes up to 13 nm. Two different deformation mechanisms are active, one is deformation through the motion of dislocations, the other is sliding in the grain boundaries. At the grain sizes studied here the latter dominates, leading to a softening as the grain size is reduced. This implies that there is an ``optimal'' grain size, where the hardness is maximal. Since the grain boundaries participate actively in the deformation, it is interesting to study the effects of introducing impurity atoms in the grain boundaries. We study how silver atoms in the grain boundaries influence the mechanical properties of nanocrystalline copper.Comment: 10 pages, LaTeX2e, PS figures and sty files included. To appear in Mater. Res. Soc. Symp. Proc. vol 538 (invited paper). For related papers, see http://www.fysik.dtu.dk/~schiotz/publist.htm

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Interstellar-medium mapping in M82 through light echoes around supernova 2014J

We present multiple-epoch measurements of the size and surface brightness of the light echoes from supernova (SN) 2014J in the nearby starburst galaxy M82. Hubble Space Telescope (HST) ACS/WFC images were taken ~277 and ~416 days after B-band maximum in the filters F475W, F606W, and F775W. Observations with HST WFC3/UVIS images at epochs ~216 and ~365 days are included for a more complete analysis. The images reveal the temporal evolution of at least two major light-echo components. The first one exhibits a filled ring structure with position-angle-dependent intensity. This radially extended, diffuse echo indicates the presence of an inhomogeneous interstellar dust cloud ranging from ~100 to ~500 pc in the foreground of the SN. The second echo component appears as an unresolved luminous quarter-circle arc centered on the SN. The wavelength dependence of scattering measured in different dust components suggests that the dust producing the luminous arc favors smaller grain sizes, while that causing the diffuse light echo may have sizes similar to those of the Milky Way dust. Smaller grains can produce an optical depth consistent with that along the supernova-Earth line of sight measured by previous studies around maximum light. Therefore, it is possible that the dust slab from which the luminous arc arises is also responsible for most of the extinction toward SN 2014J. The optical depths determined from the Milky Way-like dust in the scattering matters are lower than the optical depth produced by the dust slab