A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from ...

We review concurrent multiscale simulations of dynamic and temperature-dependent processes found in nanomechanical systems coupled to larger scale surroundings. We focus on the behavior of sub-micron MicroElectro-Mechanical Systems (MEMS), especially microresonators. These systems are often called NEMS, for Nano-Electro-Mechanical Systems. The coupling of length scales methodology we have devel...

We introduce a multiscale framework to simulate inhomogeneous fluids by coarse-graining an all-atom molecular dynamics (MD) trajectory onto sequential snapshots of hydrodynamic fields. We show that the field representation of an atomistic trajectory is quantitatively described by a dynamic field-theoretic model that couples hydrodynamic fluctuations with a Ginzburg-Landau free energy. For liqui...

We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville-von-Neumann equation approach of Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. A key ingredient of our approa...

The quasicontinuum (QC) method is a coarse-graining technique for reducing the complexity of atomistic simulations in a static and quasistatic setting. In this paper we give an a-posteriori error analysis for the quasicontinuum method in one dimension. We consider atomistic models with Lennard–Jones type finite-range interactions. We prove that, for a stable QC solution with a sufficiently smal...

Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations...

The accuracy of atomistic-to-continuum hybrid methods can be guaranteed only for deformations where the lattice configuration is stable for both the atomistic energy and the hybrid energy. For this reason, a sharp stability analysis of atomistic-to-continuum coupling methods is essential for evaluating their capabilities for predicting the formation of lattice defects. We formulate a simple one...

A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters...