Related papers: Systematic coarse graining: "Four lessons and a ca…
For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a…
The dynamics of systems subjected to noise is called Markovian in the absence of memory effects, i.e. when its immediate future only depends on its present. Time correlations in the noise source may generate non-Markovian effects that,…
With Monte Carlo simulations, we investigate the relaxation dynamics with a domain wall for magnetic systems at the critical temperature. The dynamic scaling behavior is carefully analyzed, and a dynamic roughening process is observed. For…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…
The primary objective of this work is to develop coarse-graining schemes for stochastic many-body microscopic models and quantify their effectiveness in terms of a priori and a posteriori error analysis. In this paper we focus on stochastic…
Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical…
Discrete models usually represent approximations to continuum physics. Cylindrical consistency provides a framework in which discretizations mirror exactly the continuum limit. Being a standard tool for the kinematics of loop quantum…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
Sintering, as a thermal process at elevated temperature below the melting point, is widely used to bond contacting particles into engineering products such as ceramics, metals, polymers, and cemented carbides. Modelling and simulation as…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
We present a computer-assisted approach to coarse-graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph…
Machine learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale and complexity. Given the interpolative nature of…
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…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
We present a new computational framework combining coarse-graining techniques with bootstrap methods to study quantum many-body systems. The method efficiently computes rigorous upper and lower bounds on both zero- and finite-temperature…
We present a brief survey of methods that utilize computer simulations and quantum and statistical mechanics in the analysis of electrochemical systems. The methods, Molecular Dynamics and Monte Carlo simulations and quantum-mechanical…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
I briefly review some concepts related to coarse-graining methods for the dynamics of soft matter systems and argue that such schemes will almost always need to telescope down the physical hierarchy of time-scales to a more compressed, but…