Multiscale Molecular Dynamics Approach to Energy Transfer in Nanomaterials.

After local transient fluctuations are dissipated, in an energy transfer process, a system evolves to a state where the energy density field varies slowly in time relative to the dynamics of atomic collisions and vibrations. Furthermore, the energy density field remains strongly coupled to the atomic scale processes (collisions and vibrations), and it can serve as the basis of a multiscale theory of energy transfer. Here, a method is introduced to capture the long scale energy density variations as they coevolve with the atomistic state in a way that yields insights into the basic physics and implies an efficient algorithm for energy transfer simulations.

Multiscale time-dependent density functional theory: Demonstration for plasmons.

Plasmon properties are of significant interest in pure and applied nanoscience. While time-dependent density functional theory (TDDFT) can be used to study plasmons, it becomes impractical for elucidating the effect of size, geometric arrangement, and dimensionality in complex nanosystems. In this study, a new multiscale formalism that addresses this challenge is proposed.

Reverse Coarse-Graining for Equation-Free Modeling: Application to Multiscale Molecular Dynamics.

Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this article in the context of multiscale factorization methods for molecular dynamics. These methods capture the crosstalk between atomic and coarse-grained scales arising in macromolecular systems.

Implicit Time Integration for Multiscale Molecular Dynamics Using Transcendental Padé Approximants.

Molecular dynamics systems evolve through the interplay of collective and localized disturbances. As a practical consequence, there is a restriction on the time step imposed by the broad spectrum of time scales involved. To resolve this restriction, multiscale factorization was introduced for molecular dynamics as a method that exploits the separation of time scales by coevolving the coarse-grained and atom-resolved states via Trotter factorization.

Band Propagation, Scaling Laws, and Phase Transition in a Precipitate System. 2. Computational Study.

In this second paper, we introduce a chemical kinetic model that investigates the dynamics of the experimental Ni(2+)/NH3-OH(-) Liesegang system characterized by a pattern of β-nickel hydroxide bands led by a growing pulse of α-nickel hydroxide. The model is based on a system of reaction-diffusion equations describing the precipitation reaction and dissolution of the nickel hydroxide polymorphs by ammonia. The hydroxide ions are assumed to be static whereas ammonia serves as a diffusing "vehicle" that supplies the hydroxide ions along the precipitation zone, and these ions in turn react with the static Ni(2+) ions.

Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design.

Simulations of virus-like particles needed for computer-aided vaccine design highlight the need for new algorithms that accelerate molecular dynamics. Such simulations via conventional molecular dynamics present a practical challenge due to the millions of atoms involved and the long timescales of the phenomena of interest. These phenomena include structural transitions, self-assembly, and interaction with a cell surface.

Alternating metastable/stable pattern in the mercuric iodide crystal formation outside the Ostwald Rule of Stages.

We report a reaction-diffusion system in which two initially separated electrolytes, mercuric chloride (outer) and potassium iodide (inner), interact in a solid hydrogel media to produce a propagating front of mercuric iodide precipitate. The precipitation process is accompanied by a polymorphic transformation of the kinetically favored (unstable) orange, (metastable) yellow, and (thermodynamically stable) red polymorphs of HgI2. The sequence of crystal transformation is confirmed to agree with the Ostwald Rule of Stages.

Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision.

Mesoscopic -atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. A multiscale method for simulating these systems in the friction dominated regime from the underlying -atom formulation is presented. The method integrates notions of multiscale analysis, Trotter factorization, and a hypothesis that the momenta conjugate to coarse-grained variables constitute a stationary process on the time scale of coarse-grained dynamics.

Vertex-based finite volume simulation of Liesegang patterns on structureless meshes.

A computational method is suggested for the simulation of Liesegang patterns in two dimensions on structureless meshes. The method is based on a model that incorporates dynamical equations for the nucleation and growth of solid particles of different sizes into reaction-diffusion equations. We find the model cannot be numerically solved with Galerkin-based finite element methods and cell-centered finite volume methods.

Scaling and crossover dynamics in the hyperbolic reaction-diffusion equations of initially separated components.

In this paper we investigate the dynamics of front propagation in the family of reactions (nA + mB (k)→ C) with initially segregated reactants in one dimension using hyperbolic reaction-diffusion equations with the mean-field approximation for the reaction rate. This leads to different dynamics than those predicted by their parabolic counterpart. Using perturbation techniques, we focus on the initial and intermediate temporal behavior of the center and width of the front and derive the different time scaling exponents.