Related papers: Coarse-graining schemes and a posteriori error est…
Identifying the relevant coarse-grained degrees of freedom in a complex physical system is a key stage in developing powerful effective theories in and out of equilibrium. The celebrated renormalization group provides a framework for this…
Many practical techniques for probabilistic inference require a sequence of distributions that interpolate between a tractable distribution and an intractable distribution of interest. Usually, the sequences used are simple, e.g., based on…
Equilibrium aspects of molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First an ensemble of probe molecules is designed with respect to the target…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
Choosing the optimization algorithm that performs best on a given machine learning problem is often delicate, and there is no guarantee that current state-of-the-art algorithms will perform well across all tasks. Consequently, the more…
In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo. Sensitivity analysis for stochastic systems is typically based…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Grain microstructures are crucial to the mechanical properties, performance, and often lifetime of metallic components. Hence, the prediction of grain microstructures emerging from solidification processes at relevant macroscopic scale is…
We propose a probabilistic model for refining coarse-grained spatial data by utilizing auxiliary spatial data sets. Existing methods require that the spatial granularities of the auxiliary data sets are the same as the desired granularity…
We address an iterative procedure that can be used to detect coarse-grained hyperbolic unstable equilibria (saddle points) of microscopic simulators when no equations at the macroscopic level are available. The scheme is based on the…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Fluctuating hydrodynamics provides a quantitative, large-scale description of many-body systems in terms of smooth variables, with microscopic details entering only through a small set of transport coefficients. Although this framework has…
The Weak-form Sparse Identification of Nonlinear Dynamics algorithm (WSINDy) has been demonstrated to offer coarse-graining capabilities in the context of interacting particle systems (https://doi.org/10.1016/j.physd.2022.133406). In this…
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…
We present a method that exploits self-consistent simulation of coarse-grained and fine-grained models, in order to analyse properties of physical systems. The method uses the coarse-grained model to obtain a first estimate of the quantity…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Electrostatic interactions between macroions largely govern the equilibrium thermodynamic and dynamical properties of charge-stabilized colloidal suspensions and polyelectrolyte solutions. Predicting the properties of such complex,…