Multiscale non-adiabatic dynamics with radiative decay, case study on the post-ionization fragmentation of rare-gas tetramers

In this supplementary material, we recollect, for reader's convenience, the general scheme of suggested multiscale model (Sec. 1), and basic informations about approaches used for pilot study: a detailed description of the interaction model (Sec. 2) and dynamical methods used for the dark dynamics step (Sec. 3) reported previously in two preceding studies [1, 2]. In addition, a detailed description of the treatment of radiative processes is also given (Sec. 4).Comment: supplementary material for parent paper; 9 pages, 1 figure; corrected formulae and misleading notation in Sec.4 (pages 7 and 8

New Green-Kubo formulas for transport coefficients in hard sphere-, Langevin fluids and the likes

We present generalized Green-Kubo expressions for thermal transport coefficients $\mu$ in non-conservative fluid-type systems, of the generic form, $\mu$ $= \mu_\infty$ +\int^\infty_0 dt V^{-1} \av{I_\epsilon \exp(t {\cal L}) I}_0 where $\exp(t{\cal L})$ is a pseudo-streaming operator. It consists of a sum of an instantaneous transport coefficient $\mu_\infty$, and a time integral over a time correlation function in a state of thermal equilibrium between a current $I$ and its conjugate current $I_\epsilon$. This formula with $\mu_\infty \neq 0$ and $I_\epsilon \neq I$ covers vastly different systems, such as strongly repulsive elastic interactions in hard sphere fluids, weakly interacting Langevin fluids with dissipative and stochastic interactions satisfying detailed balance conditions, and "the likes", defined in the text. For conservative systems the results reduce to the standard formulas.Comment: 7 pages, no figures. Version 2: changes in the text and references adde

Consistent particle-based algorithm with a non-ideal equation of state

A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are exactly conserved locally. The equation of state is derived and compared to independent measurements of the pressure. Results for the kinematic shear viscosity and self-diffusion constants are presented. A caging and order/disorder transition is observed at high densities and large collision frequency.Comment: 7 pages including 4 figure

Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology

For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together, leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and actions must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces.Comment: Topical review, 31 pages, 10 figure

Recognition of genetic predisposition in pediatric cancer patients: An easy-to-use selection tool

Genetic predisposition for childhood cancer is under diagnosed. Identifying these patients may lead to therapy adjustments in case of syndrome-related increased toxicity or resistant disease and syndrome-specific screening programs may lead to early detection of a further independent malignancy. Cancer surveillance might also be warranted for affected relatives and detection of a genetic mutation can allow for reproductive counseling.Here we present an easy-to-use selection tool, based on a systematic review of pediatric cancer predisposing syndromes, to identify patients who may benefit from genetic counseling. The selection tool involves five questions concerning family history, the type of malignancy, multiple primary malignancies, specific features and excessive toxicity, which results in the selection of those patients that may benefit from referral to a clinical geneticist

Transport coefficients of multi-particle collision algorithms with velocity-dependent collision rules

Detailed calculations of the transport coefficients of a recently introduced particle-based model for fluid dynamics with a non-ideal equation of state are presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are exactly conserved locally. A general scheme to derive transport coefficients for such biased, velocity dependent collision rules is developed. Analytic expressions for the self-diffusion coefficient and the shear viscosity are obtained, and very good agreement is found with numerical results at small and large mean free paths. The viscosity turns out to be proportional to the square root of temperature, as in a real gas. In addition, the theoretical framework is applied to a two-component version of the model, and expressions for the viscosity and the difference in diffusion of the two species are given.Comment: 31 pages, 8 figures, accepted by J. Phys. Cond. Matte

Capillary Rise in Nanopores: Molecular Dynamics Evidence for the Lucas-Washburn Equation

When a capillary is inserted into a liquid, the liquid will rapidly flow into it. This phenomenon, well studied and understood on the macroscale, is investigated by Molecular Dynamics simulations for coarse-grained models of nanotubes. Both a simple Lennard-Jones fluid and a model for a polymer melt are considered. In both cases after a transient period (of a few nanoseconds) the meniscus rises according to a $\sqrt{\textrm{time}}$-law. For the polymer melt, however, we find that the capillary flow exhibits a slip length $\delta$, comparable in size with the nanotube radius $R$. We show that a consistent description of the imbibition process in nanotubes is only possible upon modification of the Lucas-Washburn law which takes explicitly into account the slip length $\delta$.Comment: 4 pages 4 figure

Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures

A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are conserved locally, and entropically driven phase separation occurs for high collision rates. An explicit expression for the equation of state is derived, and the concentration dependence of the bulk free energy is shown to be the same as that of the Widom-Rowlinson model. Analytic results for the phase diagram are in excellent agreement with simulation data. Results for the line tension obtained from the analysis of the capillary wave spectrum of a droplet agree with measurements based on the Laplace's equation. The introduction of "amphiphilic" dimers makes it possible to model the phase behavior and dynamics of ternary surfactant mixtures.Comment: 7 pages including 6 figure

Evolution of displacements and strains in sheared amorphous solids

The local deformation of two-dimensional Lennard-Jones glasses under imposed shear strain is studied via computer simulations. Both the mean squared displacement and mean squared strain rise linearly with the length of the strain interval $\Delta \gamma$ over which they are measured. However, the increase in displacement does not represent single-particle diffusion. There are long-range spatial correlations in displacement associated with slip lines with an amplitude of order the particle size. Strong dependence on system size is also observed. The probability distributions of displacement and strain are very different. For small $\Delta \gamma$ the distribution of displacement has a plateau followed by an exponential tail. The distribution becomes Gaussian as $\Delta \gamma$ increases to about .03. The strain distributions consist of sharp central peaks associated with elastic regions, and long exponential tails associated with plastic regions. The latter persist to the largest $\Delta \gamma$ studied.Comment: Submitted to J. Phys. Cond. Mat. special volume for PITP Conference on Mechanical Behavior of Glassy Materials. 16 Pages, 8 figure

Particle-Based Mesoscale Hydrodynamic Techniques

Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale simulation techniques in more detail, we propose new two methods, which are intermediate between DPD and MPC -- DPD with a multibody thermostat (DPD-MT), and MPC-Langevin dynamics (MPC-LD). The key features are applying a Langevin thermostat to the relative velocities of pairs of particles or multi-particle collisions, and whether or not to employ collision cells. The viscosity of MPC-LD is derived analytically, in very good agreement with the results of numerical simulations.Comment: 7 pages, 2 figures, 1 tabl