Related papers: Understanding three-body contributions to coarse-g…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address this, we define coarse-graining units (CGU)…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
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…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
The common idea behind complexity reduction in physical systems is separation of information into "physically meaningful" and "safely ignorable". Here we consider a generic notion of such separation -- implemented by coarse-graining the…
Active matter, responsive ("smart") materials and materials under time-dependent load are systems out of thermal equilibrium. To construct coarse-grained models for such systems, one needs to integrate out a distribution of microstates that…
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…
Inspired by holographic Wilsonian renormalization, we consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, coupled via the Hamiltonian. Observations using purely long distance…
We introduce a mesoscopic partition function for classical many-body systems based on a combined spatial and phase-space coarse-graining, replacing the canonical phase-space integral with a discrete sum over occupation numbers. The…
Grain boundaries (GBs), an important constituent of polycrystalline materials, have a wide range of manifestion and significantly affect the properties of materials. Fully understanding the effects of GBs is stalemated due to lack of…
Decoding the self-assembly mechanism of metal-organic frameworks is a crucial step in reducing trial-and-error tests in their synthesis protocols. Atomistic simulations have proven essential in revealing molecular-level features of MOF…
As artificial intelligence (AI) systems are increasingly used in ethically sensitive domains such as education, healthcare, and transportation, balancing accuracy and interpretability has become a central concern. Coarse ethics (CE)…
Developing effective coarse grained (CG) approach is a promising way for studying dynamics on large size networks. In the present work, we have proposed a strength-based CG (\sCG) method to study critical phenomena of the Potts model on…
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables we…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
In molecular dynamics and sampling of high dimensional Gibbs measures coarse-graining is an important technique to reduce the dimensionality of the problem. We will study and quantify the coarse-graining error between the coarse-grained…
We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely…