A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization

Pankavich, Stephen; Ortoleva, P.

doi:10.3390/computation3010029

Cited by 1 publication

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References 55 publications

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“…The development of continuum-microstate coevolution approaches has been placed within the framework of multiscale perturbation theory; the result was Langevin equations for CG continuum variables that coevolve with the many-particle microstate. , In previous studies, multiscale factorization (MF) was developed and used to coevolve the microstate and the CG state. ,, MF carries out the microstate and CG coevolution taking into account the time scale separation between atomistic and CG dynamics, as well as the stationarity principle of atomistic fluctuations. , Most closely related to the energy transfer approach presented here is the previous work where the internal energy of a system is considered to be a slowly varying CG variable that coevolves with the rapidly fluctuating atomistic degrees of freedom . The analysis of nanosystems using density-like field variables, within a CG-microstate coevolution scheme that follows from the all-atom physics, accounts for dynamical phenomena that cannot be described by classical phenomenological continuum models which miss the intrinsic random atomic vibrations and Boltzmann distribution of velocities.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multiscale Molecular Dynamics Approach to Energy Transfer in Nanomaterials

Espinosa-Duran

Sereda

Abi-Mansour

et al. 2018

J. Chem. Theory Comput.

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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. The approach is developed based on the N-atom Liouville equation and an interatomic force field and avoids the need for conjectured phenomenological equations for energy transfer and other processes. The theory is demonstrated for sodium chloride and silicon dioxide nanoparticles immersed in a water bath via molecular dynamics simulations of the energy transfer between a nanoparticle and its aqueous host fluid. The energy density field is computed for different sets of symmetric grid densities, and the multiscale theory holds when slowly varying energy densities at the nodes are obtained. Results strongly depend on grid density and nanoparticle constituent material. A nonuniform temperature distribution, larger thermal fluctuations in the nanoparticle than in the bath, and enhancement of fluctuations at the surface, which are expressed due to the atomic nature of the systems, are captured by this method rather than by phenomenological continuum energy transfer models.

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